CSeq_loc_Conversion Class Reference

Search Toolkit Book for CSeq_loc_Conversion

#include <objmgr/impl/seq_loc_cvt.hpp>

Inheritance diagram for CSeq_loc_Conversion:

Collaboration diagram for CSeq_loc_Conversion:

Public Types
enum	EConvertFlag { eCnvDefault , eCnvAlways }
enum	ELocationType { eLocation , eProduct }
typedef CRange< TSeqPos >	TRange
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_loc_Conversion (CSeq_loc &master_loc_empty, const CSeq_id_Handle &dst_id, const CSeqMap_CI &seg, const CSeq_id_Handle &src_id, CScope *scope)
	CSeq_loc_Conversion (CSeq_loc &master_loc_empty, const CSeq_id_Handle &dst_id, const TRange &dst_rg, const CSeq_id_Handle &src_id, TSeqPos src_start, bool reverse, CScope *scope)
	~CSeq_loc_Conversion (void)
void	CombineWith (CSeq_loc_Conversion &cvt)
TSeqPos	ConvertPos (TSeqPos src_pos)
bool	GoodSrcId (const CSeq_id &id)
bool	MinusStrand (void) const
void	ConvertSimpleLoc (const CSeq_id_Handle &src_id, const CRange< TSeqPos > src_range, const SAnnotObject_Index &src_index)
bool	ConvertPoint (TSeqPos src_pos, ENa_strand src_strand)
bool	ConvertPoint (const CSeq_point &src)
bool	ConvertInterval (TSeqPos src_from, TSeqPos src_to, ENa_strand src_strand)
bool	ConvertInterval (const CSeq_interval &src)
void	ConvertFeature (CAnnotObject_Ref &ref, const CSeq_feat &orig_feat, CRef< CSeq_feat > &mapped_feat)
void	ConvertCdregion (CAnnotObject_Ref &ref, const CSeq_feat &orig_feat, CRef< CSeq_feat > &mapped_feat)
void	ConvertRna (CAnnotObject_Ref &ref, const CSeq_feat &orig_feat, CRef< CSeq_feat > &mapped_feat)
CConstRef< CInt_fuzz >	ReverseFuzz (const CInt_fuzz &fuzz) const
bool	Convert (const CSeq_loc &src, CRef< CSeq_loc > &dst, EConvertFlag flag=eCnvDefault)
void	Reset (void)
void	ResetKeepPartial (void)
bool	IsPartial (void) const
bool	HasUnconvertedId (void) const
void	SetSrcId (const CSeq_id_Handle &src)
void	SetConversion (const CSeqMap_CI &seg)
const CSeq_id_Handle &	GetSrc_id_Handle (void) const
TSeqPos	GetSrc_from (void) const
TSeqPos	GetSrc_to (void) const
const TRange &	GetTotalRange (void) const
ENa_strand	ConvertStrand (ENa_strand strand) const
void	SetMappedLocation (CAnnotObject_Ref &ref, ELocationType loctype)
void	MakeDstMix (CSeq_loc_mix &dst, const CSeq_loc_mix &src) const
const CSeq_id_Handle &	GetDst_id_Handle (void) const
const CSeq_id &	GetId (void) const
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 Member Functions
void	Convert (CAnnotObject_Ref &obj, ELocationType loctype)
void	Convert (CAnnotObject_Ref &ref, ELocationType loctype, const CSeq_id_Handle &id, const CRange< TSeqPos > &range, const SAnnotObject_Index &index)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Types
enum	EPartialFlag { fPartial_from = 1 << 0 , fPartial_to = 1 << 1 }
enum	EMappedObjectType {   eMappedObjType_not_set , eMappedObjType_Seq_loc , eMappedObjType_Seq_point , eMappedObjType_Seq_interval ,   eMappedObjType_Seq_loc_mix }
typedef int	TPartialFlag

Private Member Functions
void	CheckDstInterval (void)
void	CheckDstPoint (void)
void	CheckDstMix (void)
CRef< CSeq_interval >	GetDstInterval (void)
CRef< CSeq_point >	GetDstPoint (void)
CRef< CSeq_loc_mix >	GetDstMix (void)
void	SetDstLoc (CRef< CSeq_loc > &loc)
bool	IsSpecialLoc (void) const
CSeq_loc &	GetDstLocEmpty (void)
CSeq_id &	GetDstId (void)
TRange	GetDstRange (void)
TRange	GetSrcRange (void) const
void	ConvertPacked_int (const CSeq_loc &src, CRef< CSeq_loc > &dst)
void	ConvertPacked_pnt (const CSeq_loc &src, CRef< CSeq_loc > &dst)
bool	ConvertSimpleMix (const CSeq_loc &src)
void	ConvertMix (const CSeq_loc &src, CRef< CSeq_loc > &dst, EConvertFlag flag=eCnvDefault)
void	ConvertEquiv (const CSeq_loc &src, CRef< CSeq_loc > &dst)
void	ConvertBond (const CSeq_loc &src, CRef< CSeq_loc > &dst)

Static Private Member Functions
static CSeq_loc_mix::Tdata *	s_ConvertToMix (CRef< CSeq_loc > &loc)

Private Attributes
CSeq_id_Handle	m_Src_id_Handle
TSeqPos	m_Src_from
TSeqPos	m_Src_to
TSignedSeqPos	m_Shift
bool	m_Reverse
CSeq_id_Handle	m_Dst_id_Handle
CRef< CSeq_loc >	m_Dst_loc_Empty
TRange	m_TotalRange
bool	m_Partial
bool	m_PartialHasUnconvertedId
TPartialFlag	m_PartialFlag
CConstRef< CInt_fuzz >	m_DstFuzz_from
CConstRef< CInt_fuzz >	m_DstFuzz_to
EMappedObjectType	m_LastType
TRange	m_LastRange
ENa_strand	m_LastStrand
CConstRef< CSeq_loc >	m_SrcLoc
CHeapScope	m_Scope
CRef< CGraphRanges >	m_GraphRanges

Friends
class	CAnnot_Collector
class	CSeq_loc_Conversion_Set
class	CSeq_align_Mapper
struct	CConversionRef_Less

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

Definition at line 76 of file seq_loc_cvt.hpp.

Member Typedef Documentation

TPartialFlag

typedef int CSeq_loc_Conversion::TPartialFlag

private

Definition at line 273 of file seq_loc_cvt.hpp.

TRange

typedef CRange<TSeqPos> CSeq_loc_Conversion::TRange

Definition at line 79 of file seq_loc_cvt.hpp.

Member Enumeration Documentation

EConvertFlag

enum CSeq_loc_Conversion::EConvertFlag

Enumerator
eCnvDefault
eCnvAlways

Definition at line 132 of file seq_loc_cvt.hpp.

ELocationType

enum CSeq_loc_Conversion::ELocationType

Enumerator
eLocation
eProduct

Definition at line 136 of file seq_loc_cvt.hpp.

EMappedObjectType

enum CSeq_loc_Conversion::EMappedObjectType

private

Enumerator
eMappedObjType_not_set
eMappedObjType_Seq_loc
eMappedObjType_Seq_point
eMappedObjType_Seq_interval
eMappedObjType_Seq_loc_mix

Definition at line 280 of file seq_loc_cvt.hpp.

EPartialFlag

enum CSeq_loc_Conversion::EPartialFlag

private

Enumerator
fPartial_from
fPartial_to

Definition at line 269 of file seq_loc_cvt.hpp.

Constructor & Destructor Documentation

CSeq_loc_Conversion() [1/2]

CSeq_loc_Conversion::CSeq_loc_Conversion	(	CSeq_loc &	master_loc_empty,
		const CSeq_id_Handle &	dst_id,
		const CSeqMap_CI &	seg,
		const CSeq_id_Handle &	src_id,
		CScope *	scope
	)

Definition at line 64 of file seq_loc_cvt.cpp.

CSeq_loc_Conversion() [2/2]

CSeq_loc_Conversion::CSeq_loc_Conversion	(	CSeq_loc &	master_loc_empty,
		const CSeq_id_Handle &	dst_id,
		const TRange &	dst_rg,
		const CSeq_id_Handle &	src_id,
		TSeqPos	src_start,
		bool	reverse,
		CScope *	scope
	)

Definition at line 88 of file seq_loc_cvt.cpp.

References CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), m_Reverse, m_Shift, m_Src_from, m_Src_to, and Reset().

~CSeq_loc_Conversion()

CSeq_loc_Conversion::~CSeq_loc_Conversion

(

void

)

Definition at line 121 of file seq_loc_cvt.cpp.

References _ASSERT, and IsSpecialLoc().

Member Function Documentation

CheckDstInterval()

void CSeq_loc_Conversion::CheckDstInterval ( void  )

inlineprivate

Definition at line 413 of file seq_loc_cvt.cpp.

References eMappedObjType_not_set, eMappedObjType_Seq_interval, m_LastType, and NCBI_THROW.

Referenced by GetDstInterval().

CheckDstMix()

void CSeq_loc_Conversion::CheckDstMix ( void  )

inlineprivate

Definition at line 435 of file seq_loc_cvt.cpp.

References eMappedObjType_not_set, eMappedObjType_Seq_loc_mix, m_LastType, and NCBI_THROW.

Referenced by GetDstMix().

CheckDstPoint()

void CSeq_loc_Conversion::CheckDstPoint ( void  )

inlineprivate

Definition at line 424 of file seq_loc_cvt.cpp.

References eMappedObjType_not_set, eMappedObjType_Seq_point, m_LastType, and NCBI_THROW.

Referenced by GetDstPoint().

CombineWith()

void CSeq_loc_Conversion::CombineWith

(

CSeq_loc_Conversion &

cvt

)

Definition at line 146 of file seq_loc_cvt.cpp.

References _ASSERT, ConvertPos(), COpenRange< Position >::Empty(), GetDstRange(), CRange_Base::GetFrom(), GetSrcRange(), CRange_Base::GetTo(), kInvalidSeqPos, m_Dst_id_Handle, m_Dst_loc_Empty, m_Reverse, m_Shift, m_Src_from, m_Src_id_Handle, m_Src_to, and Reset().

Referenced by CAnnot_Collector::x_SearchRange().

Convert() [1/3]

void CSeq_loc_Conversion::Convert ( CAnnotObject_Ref &  obj, ELocationType  loctype  )

protected

Definition at line 1173 of file seq_loc_cvt.cpp.

References _ASSERT, Convert(), ConvertFeature(), CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, eLocation, CAnnotObject_Ref::GetAnnotObject_Info(), CAnnotObject_Info::GetFeatFast(), CAnnotObject_Info::GetGraphFast(), CSeq_graph_Base::GetLoc(), CSeq_feat_Base::GetLocation(), CAnnotObject_Ref::GetMappingInfo(), CRef< C, Locker >::GetPointerOrNull(), CSeq_feat_Base::GetProduct(), CAnnotObject_Info::GetSeq_annot_Info(), CAnnotObject_Info::IsRegular(), m_GraphRanges, NeedFullFeature(), CRef< C, Locker >::Reset(), Reset(), CAnnotMapping_Info::SetGraphRanges(), SetMappedLocation(), CAnnotMapping_Info::SetMappedSeq_feat(), CAnnotMapping_Info::SetMappedSeq_loc(), CSeq_annot_Info::UpdateTableFeat(), CSeq_annot_Info::UpdateTableFeatLocation(), CSeq_annot_Info::UpdateTableFeatProduct(), and CAnnotObject_Info::Which().

Convert() [2/3]

void CSeq_loc_Conversion::Convert ( CAnnotObject_Ref &  ref, ELocationType  loctype, const CSeq_id_Handle &  id, const CRange< TSeqPos > &  range, const SAnnotObject_Index &  index  )

protected

Definition at line 1267 of file seq_loc_cvt.cpp.

References _ASSERT, Convert(), ConvertFeature(), ConvertSimpleLoc(), CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CSeq_annot_Base::C_Data::e_Seq_table, eCnvAlways, eLocation, CAnnotObject_Ref::GetAnnotObject_Info(), CAnnotObject_Info::GetFeatFast(), CAnnotObject_Info::GetGraphFast(), CSeq_graph_Base::GetLoc(), CSeq_feat_Base::GetLocation(), CAnnotObject_Ref::GetMappingInfo(), CRef< C, Locker >::GetPointerOrNull(), CSeq_feat_Base::GetProduct(), CAnnotObject_Info::GetSeq_annot_Info(), CSeq_annot_Info::GetTableInfo(), CAnnotObject_Info::IsRegular(), SAnnotObject_Index::LocationIsSimple(), m_GraphRanges, NeedFullFeature(), compile_time_bits::range(), CRef< C, Locker >::Reset(), Reset(), CAnnotMapping_Info::SetGraphRanges(), SetMappedLocation(), CAnnotMapping_Info::SetMappedSeq_feat(), CAnnotMapping_Info::SetMappedSeq_loc(), table, CSeq_annot_Info::UpdateTableFeat(), CSeq_annot_Info::UpdateTableFeatLocation(), CSeq_annot_Info::UpdateTableFeatProduct(), and CAnnotObject_Info::Which().

Convert() [3/3]

bool CSeq_loc_Conversion::Convert	(	const CSeq_loc &	src,
		CRef< CSeq_loc > &	dst,
		EConvertFlag	flag = eCnvDefault
	)

Definition at line 878 of file seq_loc_cvt.cpp.

References _ASSERT, ConvertBond(), ConvertEquiv(), ConvertInterval(), ConvertMix(), ConvertPacked_int(), ConvertPacked_pnt(), ConvertPoint(), CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, eCnvAlways, CScope::eGetBioseq_All, eMappedObjType_Seq_loc, eNa_strand_unknown, CScope_Impl::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), GetDstId(), CSeq_loc_Base::GetEmpty(), CSeq_id_Handle::GetHandle(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPnt(), CSeq_loc_Base::GetWhole(), GoodSrcId(), CGraphRanges::IncOffset(), IsSpecialLoc(), m_GraphRanges, m_LastType, m_Scope, NCBI_THROW, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), SetDstLoc(), CSeq_loc::SetEmpty(), CSeq_loc::SetNull(), and CSeq_loc_Base::Which().

Referenced by CSeq_loc_Conversion_Set::Convert(), Convert(), ConvertCdregion(), ConvertEquiv(), ConvertMix(), ConvertRna(), and CAnnot_Collector::x_SearchRange().

ConvertBond()

void CSeq_loc_Conversion::ConvertBond ( const CSeq_loc &  src, CRef< CSeq_loc > &  dst  )

private

Definition at line 851 of file seq_loc_cvt.cpp.

References _ASSERT, ConvertPoint(), CSeq_loc_Base::e_Bond, CSeq_bond_Base::GetA(), CSeq_bond_Base::GetB(), CSeq_loc_Base::GetBond(), GetDstPoint(), CSeq_bond_Base::IsSetB(), CRef< C, Locker >::Reset(), CSeq_bond_Base::SetA(), CSeq_bond_Base::SetB(), CSeq_loc::SetBond(), and CSeq_loc_Base::Which().

Referenced by Convert().

ConvertCdregion()

void CSeq_loc_Conversion::ConvertCdregion	(	CAnnotObject_Ref &	ref,
		const CSeq_feat &	orig_feat,
		CRef< CSeq_feat > &	mapped_feat
	)

Definition at line 971 of file seq_loc_cvt.cpp.

References _ASSERT, Convert(), CSeq_loc_Base::e_not_set, eCnvAlways, CAnnotObject_Ref::GetAnnotObject_Info(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CCdregion_Base::GetCode_break(), CCdregion_Base::GetConflict(), CSeq_feat_Base::GetData(), CAnnotObject_Info::GetFeatFast(), CCdregion_Base::GetFrame(), CCdregion_Base::GetGaps(), CAnnotObject_Ref::GetMappingInfo(), CCdregion_Base::GetMismatch(), CCdregion_Base::GetOrf(), CCdregion_Base::GetStops(), CAnnotMapping_Info::InitializeMappedSeq_feat(), CSeqFeatData_Base::IsCdregion(), CAnnotObject_Info::IsFeat(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetCode_break(), CCdregion_Base::IsSetConflict(), CCdregion_Base::IsSetFrame(), CCdregion_Base::IsSetGaps(), CCdregion_Base::IsSetMismatch(), CCdregion_Base::IsSetOrf(), CCdregion_Base::IsSetStops(), ITERATE, CRef< C, Locker >::Reset(), CCdregion_Base::ResetCode(), CCdregion_Base::ResetConflict(), CCdregion_Base::ResetFrame(), CCdregion_Base::ResetGaps(), ResetKeepPartial(), CCdregion_Base::ResetMismatch(), CCdregion_Base::ResetOrf(), CCdregion_Base::ResetStops(), CCode_break_Base::SetAa(), CSeqFeatData::SetCdregion(), CCdregion_Base::SetCode(), CCdregion_Base::SetCode_break(), CCdregion_Base::SetConflict(), CSeq_feat_Base::SetData(), CCdregion_Base::SetFrame(), CCdregion_Base::SetGaps(), CCode_break_Base::SetLoc(), CCdregion_Base::SetMismatch(), CCdregion_Base::SetOrf(), CCdregion_Base::SetStops(), and CSeq_loc_Base::Which().

Referenced by ConvertFeature().

ConvertEquiv()

void CSeq_loc_Conversion::ConvertEquiv ( const CSeq_loc &  src, CRef< CSeq_loc > &  dst  )

private

Definition at line 827 of file seq_loc_cvt.cpp.

References _ASSERT, Convert(), CSeq_loc_Base::e_Equiv, eCnvAlways, CSeq_loc_equiv_Base::Get(), CSeq_loc_Base::GetEquiv(), CSeq_loc_Mapper_Base::GetNonMappingAsNull(), i, ITERATE, CRef< C, Locker >::Reset(), CSeq_loc::SetEquiv(), CSeq_loc::SetNull(), and CSeq_loc_Base::Which().

Referenced by Convert().

ConvertFeature()

void CSeq_loc_Conversion::ConvertFeature	(	CAnnotObject_Ref &	ref,
		const CSeq_feat &	orig_feat,
		CRef< CSeq_feat > &	mapped_feat
	)

Definition at line 1156 of file seq_loc_cvt.cpp.

References ConvertCdregion(), ConvertRna(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Rna, CSeq_feat_Base::GetData(), and CSeqFeatData_Base::Which().

Referenced by Convert().

ConvertInterval() [1/2]

bool CSeq_loc_Conversion::ConvertInterval

(

const CSeq_interval &

src

)

Definition at line 289 of file seq_loc_cvt.cpp.

References ConvertInterval(), CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, fPartial_from, fPartial_to, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CSeq_interval::GetLength(), CInt_fuzz_Base::GetLim(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), GoodSrcId(), CGraphRanges::IncOffset(), CInt_fuzz_Base::IsLim(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetStrand(), m_DstFuzz_from, m_DstFuzz_to, m_GraphRanges, m_PartialFlag, m_Reverse, CConstRef< C, Locker >::Reset(), and ReverseFuzz().

ConvertInterval() [2/2]

bool CSeq_loc_Conversion::ConvertInterval	(	TSeqPos	src_from,
		TSeqPos	src_to,
		ENa_strand	src_strand
	)

Definition at line 360 of file seq_loc_cvt.cpp.

References _ASSERT, CGraphRanges::AddRange(), eMappedObjType_Seq_interval, fPartial_from, fPartial_to, CGraphRanges::IncOffset(), IsSpecialLoc(), len, m_DstFuzz_from, m_DstFuzz_to, m_GraphRanges, m_LastRange, m_LastStrand, m_LastType, m_Partial, m_PartialFlag, m_Reverse, m_Shift, m_Src_from, m_Src_to, m_TotalRange, CConstRef< C, Locker >::Reset(), Reverse(), CRange_Base::SetFrom(), COpenRange< Position >::SetLength(), and swap().

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), Convert(), ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertPacked_int(), ConvertSimpleLoc(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

ConvertMix()

void CSeq_loc_Conversion::ConvertMix ( const CSeq_loc &  src, CRef< CSeq_loc > &  dst, EConvertFlag  flag = eCnvDefault  )

private

Definition at line 786 of file seq_loc_cvt.cpp.

References _ASSERT, Convert(), ConvertSimpleMix(), CSeq_loc_Base::e_Mix, eCnvAlways, eExtreme_Biological, CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetMix(), CSeq_loc_Mapper_Base::GetNonMappingAsNull(), i, CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), ITERATE, s_ConvertToMix(), CSeq_loc::SetNull(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), and CSeq_loc_Base::Which().

Referenced by Convert().

ConvertPacked_int()

void CSeq_loc_Conversion::ConvertPacked_int ( const CSeq_loc &  src, CRef< CSeq_loc > &  dst  )

private

Definition at line 567 of file seq_loc_cvt.cpp.

References _ASSERT, ConvertInterval(), CSeq_loc_Base::e_Packed_int, eExtreme_Biological, CPacked_seqint_Base::Get(), GetDstInterval(), CSeq_loc_Mapper_Base::GetNonMappingAsNull(), CSeq_loc_Base::GetPacked_int(), i, CSeq_interval::IsPartialStart(), CSeq_loc::IsPartialStop(), ITERATE, CRef< C, Locker >::Reset(), s_ConvertToMix(), CSeq_loc::SetInt(), CSeq_loc::SetNull(), CSeq_loc::SetPacked_int(), CSeq_interval::SetPartialStart(), CSeq_loc::SetPartialStop(), and CSeq_loc_Base::Which().

Referenced by Convert().

ConvertPacked_pnt()

void CSeq_loc_Conversion::ConvertPacked_pnt ( const CSeq_loc &  src, CRef< CSeq_loc > &  dst  )

private

Definition at line 616 of file seq_loc_cvt.cpp.

References _ASSERT, CSerialObject::Assign(), ConvertPos(), ConvertStrand(), CSeq_loc_Base::e_Packed_pnt, eNa_strand_unknown, GetDstId(), CPacked_seqpnt_Base::GetFuzz(), CPacked_seqpnt_Base::GetId(), CSeq_loc_Mapper_Base::GetNonMappingAsNull(), CSeq_loc_Base::GetPacked_pnt(), CPacked_seqpnt_Base::GetPoints(), CPacked_seqpnt_Base::GetStrand(), GoodSrcId(), i, CGraphRanges::IncOffset(), CPacked_seqpnt_Base::IsSetFuzz(), CPacked_seqpnt_Base::IsSetStrand(), ITERATE, kInvalidSeqPos, m_GraphRanges, m_Reverse, m_TotalRange, CRef< C, Locker >::Reset(), ReverseFuzz(), s_ConvertToMix(), CPacked_seqpnt_Base::SetFuzz(), CPacked_seqpnt_Base::SetId(), CSeq_loc::SetNull(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CPacked_seqpnt_Base::SetPoints(), CPacked_seqpnt_Base::SetStrand(), and CSeq_loc_Base::Which().

Referenced by Convert().

ConvertPoint() [1/2]

bool CSeq_loc_Conversion::ConvertPoint

(

const CSeq_point &

src

)

Definition at line 262 of file seq_loc_cvt.cpp.

References ConvertPoint(), CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, fPartial_from, CSeq_point_Base::GetFuzz(), CSeq_point_Base::GetId(), CInt_fuzz_Base::GetLim(), CSeq_point_Base::GetPoint(), CSeq_point_Base::GetStrand(), GoodSrcId(), CGraphRanges::IncOffset(), CInt_fuzz_Base::IsLim(), CSeq_point_Base::IsSetFuzz(), CSeq_point_Base::IsSetStrand(), m_DstFuzz_from, m_GraphRanges, m_PartialFlag, m_Reverse, CConstRef< C, Locker >::Reset(), and ReverseFuzz().

ConvertPoint() [2/2]

bool CSeq_loc_Conversion::ConvertPoint	(	TSeqPos	src_pos,
		ENa_strand	src_strand
	)

Definition at line 330 of file seq_loc_cvt.cpp.

References _ASSERT, CGraphRanges::AddRange(), eMappedObjType_Seq_point, CGraphRanges::IncOffset(), IsSpecialLoc(), m_DstFuzz_from, m_DstFuzz_to, m_GraphRanges, m_LastRange, m_LastStrand, m_LastType, m_Partial, m_PartialFlag, m_Reverse, m_Shift, m_Src_to, m_TotalRange, CConstRef< C, Locker >::Reset(), Reverse(), and CRange_Base::SetFrom().

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), Convert(), ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), ConvertPoint(), CSeq_loc_Conversion_Set::ConvertPoint(), and ConvertSimpleLoc().

ConvertPos()

TSeqPos CSeq_loc_Conversion::ConvertPos ( TSeqPos  src_pos )

inline

Definition at line 408 of file seq_loc_cvt.hpp.

References kInvalidSeqPos, m_Partial, m_Reverse, m_Shift, and m_Src_to.

Referenced by CombineWith(), ConvertPacked_pnt(), and GetDstRange().

ConvertRna()

void CSeq_loc_Conversion::ConvertRna	(	CAnnotObject_Ref &	ref,
		const CSeq_feat &	orig_feat,
		CRef< CSeq_feat > &	mapped_feat
	)

Definition at line 1060 of file seq_loc_cvt.cpp.

References _ASSERT, CSerialObject::Assign(), Convert(), CSeq_loc_Base::e_not_set, eCnvAlways, eShallow, CTrna_ext_Base::GetAa(), CAnnotObject_Ref::GetAnnotObject_Info(), CTrna_ext_Base::GetAnticodon(), CTrna_ext_Base::GetCodon(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CAnnotObject_Info::GetFeatFast(), CAnnotObject_Ref::GetMappingInfo(), CRNA_ref_Base::GetPseudo(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::C_Ext::GetTRNA(), CRNA_ref_Base::GetType(), CAnnotMapping_Info::InitializeMappedSeq_feat(), CAnnotObject_Info::IsFeat(), CSeqFeatData_Base::IsRna(), CTrna_ext_Base::IsSetAnticodon(), CTrna_ext_Base::IsSetCodon(), CRNA_ref_Base::IsSetExt(), CRNA_ref_Base::IsSetPseudo(), CRNA_ref_Base::C_Ext::IsTRNA(), CRef< C, Locker >::Reset(), ResetKeepPartial(), CSeq_feat_Base::SetData(), and CSeq_loc_Base::Which().

Referenced by ConvertFeature().

ConvertSimpleLoc()

void CSeq_loc_Conversion::ConvertSimpleLoc	(	const CSeq_id_Handle &	src_id,
		const CRange< TSeqPos >	src_range,
		const SAnnotObject_Index &	src_index
	)

Definition at line 226 of file seq_loc_cvt.cpp.

References _ASSERT, ConvertInterval(), ConvertPoint(), CScope::eGetBioseq_All, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, SAnnotObject_Index::fStrand_mask, SAnnotObject_Index::fStrand_minus, SAnnotObject_Index::fStrand_plus, CScope_Impl::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CRange_Base::GetFrom(), CRange_Base::GetTo(), SAnnotObject_Index::LocationIsInterval(), SAnnotObject_Index::LocationIsPoint(), SAnnotObject_Index::LocationIsWhole(), SAnnotObject_Index::m_Flags, m_Partial, m_PartialHasUnconvertedId, m_Scope, and m_Src_id_Handle.

Referenced by Convert().

ConvertSimpleMix()

bool CSeq_loc_Conversion::ConvertSimpleMix ( const CSeq_loc &  src )

private

Definition at line 688 of file seq_loc_cvt.cpp.

References CSeq_loc::begin(), eMappedObjType_Seq_loc_mix, eNa_strand_unknown, CSeq_loc_mix_Base::Get(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), GoodSrcId(), i, CSeq_loc_Base::IsInt(), IsReverse(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetStrand(), ITERATE, m_DstFuzz_from, m_DstFuzz_to, m_LastRange, m_LastStrand, m_LastType, m_PartialFlag, m_Reverse, m_Shift, m_Src_from, m_Src_to, m_SrcLoc, m_TotalRange, CConstRef< C, Locker >::Reset(), Reverse(), and CRange_Base::SetFrom().

Referenced by ConvertMix().

ConvertStrand()

ENa_strand CSeq_loc_Conversion::ConvertStrand ( ENa_strand  strand ) const

inline

Definition at line 437 of file seq_loc_cvt.hpp.

References m_Reverse, and Reverse().

Referenced by ConvertPacked_pnt().

GetDst_id_Handle()

const CSeq_id_Handle& CSeq_loc_Conversion::GetDst_id_Handle ( void  ) const

inline

Definition at line 185 of file seq_loc_cvt.hpp.

References m_Dst_id_Handle.

Referenced by CSeq_loc_Conversion_Set::Add().

GetDstId()

CSeq_id& CSeq_loc_Conversion::GetDstId ( void  )

inlineprivate

Definition at line 222 of file seq_loc_cvt.hpp.

References m_Dst_loc_Empty, and CSeq_loc::SetEmpty().

Referenced by Convert(), CSeq_loc_Conversion_Set::Convert(), ConvertPacked_pnt(), GetDstInterval(), GetDstPoint(), and SetMappedLocation().

GetDstInterval()

CRef< CSeq_interval > CSeq_loc_Conversion::GetDstInterval ( void  )

private

Definition at line 445 of file seq_loc_cvt.cpp.

References CheckDstInterval(), CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, fPartial_from, fPartial_to, GetDstId(), CRange_Base::GetFrom(), CRange_Base::GetTo(), m_DstFuzz_from, m_DstFuzz_to, m_LastRange, m_LastStrand, m_PartialFlag, CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().

Referenced by CSeq_loc_Conversion_Set::ConvertInterval(), ConvertPacked_int(), and SetDstLoc().

GetDstLocEmpty()

CSeq_loc& CSeq_loc_Conversion::GetDstLocEmpty ( void  )

inlineprivate

Definition at line 218 of file seq_loc_cvt.hpp.

References m_Dst_loc_Empty.

GetDstMix()

CRef< CSeq_loc_mix > CSeq_loc_Conversion::GetDstMix ( void  )

private

Definition at line 529 of file seq_loc_cvt.cpp.

References CheckDstMix(), CSeq_loc_Base::GetMix(), m_SrcLoc, MakeDstMix(), and CConstRef< C, Locker >::Reset().

Referenced by SetDstLoc().

GetDstPoint()

CRef< CSeq_point > CSeq_loc_Conversion::GetDstPoint ( void  )

private

Definition at line 472 of file seq_loc_cvt.cpp.

References _ASSERT, CheckDstPoint(), CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, fPartial_from, GetDstId(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), m_DstFuzz_from, m_LastRange, m_LastStrand, m_PartialFlag, CSeq_point_Base::SetFuzz(), CSeq_point_Base::SetId(), CSeq_point_Base::SetPoint(), and CSeq_point_Base::SetStrand().

Referenced by ConvertBond(), CSeq_loc_Conversion_Set::ConvertBond(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPoint(), and SetDstLoc().

GetDstRange()

TRange CSeq_loc_Conversion::GetDstRange ( void  )

inlineprivate

Definition at line 227 of file seq_loc_cvt.hpp.

References ConvertPos(), m_Reverse, m_Src_from, and m_Src_to.

Referenced by CombineWith().

GetId()

const CSeq_id& CSeq_loc_Conversion::GetId ( void  ) const

inline

Definition at line 189 of file seq_loc_cvt.hpp.

References CSeq_loc_Base::GetEmpty(), and m_Dst_loc_Empty.

Referenced by CAnnotMapping_Info::GetLocationId().

GetSrc_from()

TSeqPos CSeq_loc_Conversion::GetSrc_from ( void  ) const

inline

Definition at line 166 of file seq_loc_cvt.hpp.

References m_Src_from.

Referenced by CSeq_loc_Conversion_Set::ConvertInterval(), and CSeq_loc_Conversion_Set::x_Add().

GetSrc_id_Handle()

const CSeq_id_Handle& CSeq_loc_Conversion::GetSrc_id_Handle ( void  ) const

inline

Definition at line 162 of file seq_loc_cvt.hpp.

References m_Src_id_Handle.

Referenced by CSeq_loc_Conversion_Set::x_Add().

GetSrc_to()

TSeqPos CSeq_loc_Conversion::GetSrc_to ( void  ) const

inline

Definition at line 170 of file seq_loc_cvt.hpp.

References m_Src_to.

Referenced by CSeq_loc_Conversion_Set::ConvertInterval(), and CSeq_loc_Conversion_Set::x_Add().

GetSrcRange()

TRange CSeq_loc_Conversion::GetSrcRange ( void  ) const

inlineprivate

Definition at line 233 of file seq_loc_cvt.hpp.

References m_Src_from, and m_Src_to.

Referenced by CombineWith().

GetTotalRange()

const TRange& CSeq_loc_Conversion::GetTotalRange ( void  ) const

inline

Definition at line 175 of file seq_loc_cvt.hpp.

References m_TotalRange.

Referenced by CSeq_loc_Conversion_Set::Convert(), CSeq_loc_Conversion_Set::ConvertBond(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), and CSeq_loc_Conversion_Set::ConvertPoint().

GoodSrcId()

bool CSeq_loc_Conversion::GoodSrcId ( const CSeq_id &  id )

inline

Definition at line 426 of file seq_loc_cvt.hpp.

References m_Partial, m_PartialHasUnconvertedId, and m_Src_id_Handle.

Referenced by Convert(), CSeq_loc_Conversion_Set::Convert(), ConvertInterval(), ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), ConvertPoint(), and ConvertSimpleMix().

HasUnconvertedId()

bool CSeq_loc_Conversion::HasUnconvertedId ( void  ) const

inline

Definition at line 151 of file seq_loc_cvt.hpp.

References m_PartialHasUnconvertedId.

Referenced by CSeq_loc_Conversion_Set::Convert().

IsPartial()

bool CSeq_loc_Conversion::IsPartial ( void  ) const

inline

Definition at line 147 of file seq_loc_cvt.hpp.

References m_Partial.

Referenced by CSeq_loc_Conversion_Set::Convert(), CAnnot_Collector::x_AddObject(), and CAnnot_Collector::x_AddObjectMapping().

IsSpecialLoc()

bool CSeq_loc_Conversion::IsSpecialLoc ( void  ) const

inlineprivate

Definition at line 401 of file seq_loc_cvt.hpp.

References eMappedObjType_Seq_point, and m_LastType.

Referenced by Convert(), ConvertInterval(), ConvertPoint(), ResetKeepPartial(), SetDstLoc(), SetMappedLocation(), and ~CSeq_loc_Conversion().

MakeDstMix()

void CSeq_loc_Conversion::MakeDstMix	(	CSeq_loc_mix &	dst,
		const CSeq_loc_mix &	src
	)		const

Definition at line 494 of file seq_loc_cvt.cpp.

References eNa_strand_unknown, CSeq_loc_mix_Base::Get(), CSeq_interval_Base::GetFrom(), CRef< C, Locker >::GetNCObject(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_interval_Base::IsSetStrand(), ITERATE, m_Dst_loc_Empty, m_Reverse, m_Shift, Reverse(), CSeq_loc_mix_Base::Set(), CSeq_loc::SetEmpty(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_loc::SetInt(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().

Referenced by GetDstMix(), and CAnnotMapping_Info::UpdateMappedSeq_loc().

MinusStrand()

bool CSeq_loc_Conversion::MinusStrand ( void  ) const

inline

Definition at line 105 of file seq_loc_cvt.hpp.

References m_Reverse.

Reset()

void CSeq_loc_Conversion::Reset

(

void

)

Definition at line 138 of file seq_loc_cvt.cpp.

References m_Partial, m_PartialHasUnconvertedId, and ResetKeepPartial().

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), CombineWith(), Convert(), CSeq_loc_Conversion_Set::Convert(), CSeq_loc_Conversion_Set::ConvertBond(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPoint(), and CSeq_loc_Conversion().

ResetKeepPartial()

void CSeq_loc_Conversion::ResetKeepPartial

(

void

)

Definition at line 127 of file seq_loc_cvt.cpp.

References _ASSERT, COpenRange< TSeqPos >::GetEmpty(), IsSpecialLoc(), m_DstFuzz_from, m_DstFuzz_to, m_GraphRanges, m_PartialFlag, m_TotalRange, CRef< C, Locker >::Reset(), and CConstRef< C, Locker >::Reset().

Referenced by ConvertCdregion(), ConvertRna(), and Reset().

ReverseFuzz()

CConstRef< CInt_fuzz > CSeq_loc_Conversion::ReverseFuzz

(

const CInt_fuzz &

fuzz

)

const

Definition at line 207 of file seq_loc_cvt.cpp.

References ConstRef(), CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), and CInt_fuzz_Base::SetLim().

Referenced by ConvertInterval(), ConvertPacked_pnt(), and ConvertPoint().

s_ConvertToMix()

CSeq_loc_mix::Tdata * CSeq_loc_Conversion::s_ConvertToMix ( CRef< CSeq_loc > &  loc )

staticprivate

Definition at line 1424 of file seq_loc_cvt.cpp.

References CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::IsMix(), CPacked_seqpnt_Base::IsSetFuzz(), CPacked_seqpnt_Base::IsSetStrand(), NON_CONST_ITERATE, pi, CRef< C, Locker >::Reset(), CPacked_seqpnt_Base::SetFuzz(), CPacked_seqpnt_Base::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CPacked_seqpnt_Base::SetPoints(), CPacked_seqpnt_Base::SetStrand(), and CSeq_loc_Base::Which().

Referenced by ConvertMix(), ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), and ConvertPacked_pnt().

SetConversion()

void CSeq_loc_Conversion::SetConversion

(

const CSeqMap_CI &

seg

)

Definition at line 192 of file seq_loc_cvt.cpp.

References CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), m_Reverse, m_Shift, m_Src_from, and m_Src_to.

SetDstLoc()

void CSeq_loc_Conversion::SetDstLoc ( CRef< CSeq_loc > &  loc )

private

Definition at line 539 of file seq_loc_cvt.cpp.

References _ASSERT, eMappedObjType_Seq_interval, eMappedObjType_Seq_loc_mix, eMappedObjType_Seq_point, GetDstInterval(), GetDstMix(), GetDstPoint(), IsSpecialLoc(), m_LastType, CRef< C, Locker >::Reset(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), and CSeq_loc::SetPnt().

Referenced by Convert(), and SetMappedLocation().

SetMappedLocation()

void CSeq_loc_Conversion::SetMappedLocation	(	CAnnotObject_Ref &	ref,
		ELocationType	loctype
	)

Definition at line 1382 of file seq_loc_cvt.cpp.

References CAnnotMapping_Info::eMappedObjType_not_set, eMappedObjType_not_set, eMappedObjType_Seq_loc_mix, eMappedObjType_Seq_point, eProduct, fPartial_from, fPartial_to, GetDstId(), CAnnotMapping_Info::GetMappedObjectType(), CAnnotObject_Ref::GetMappingInfo(), CAnnotMapping_Info::IsPartial(), IsSpecialLoc(), m_Dst_loc_Empty, m_DstFuzz_from, m_DstFuzz_to, m_LastStrand, m_LastType, m_Partial, m_PartialFlag, m_TotalRange, SetDstLoc(), CAnnotMapping_Info::SetMappedConverstion(), CAnnotMapping_Info::SetMappedPartial_from(), CAnnotMapping_Info::SetMappedPartial_to(), CAnnotMapping_Info::SetMappedSeq_id(), CAnnotMapping_Info::SetMappedSeq_loc(), CAnnotMapping_Info::SetMappedStrand(), CAnnotMapping_Info::SetPartial(), CAnnotMapping_Info::SetProduct(), and CAnnotMapping_Info::SetTotalRange().

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), and Convert().

SetSrcId()

void CSeq_loc_Conversion::SetSrcId ( const CSeq_id_Handle &  src )

inline

Definition at line 156 of file seq_loc_cvt.hpp.

References m_Src_id_Handle.

Referenced by CAnnot_Collector::x_SearchTSE2().

Friends And Related Function Documentation

CAnnot_Collector

friend class CAnnot_Collector

friend

Definition at line 195 of file seq_loc_cvt.hpp.

CConversionRef_Less

friend struct CConversionRef_Less

friend

Definition at line 299 of file seq_loc_cvt.hpp.

CSeq_align_Mapper

friend class CSeq_align_Mapper

friend

Definition at line 298 of file seq_loc_cvt.hpp.

CSeq_loc_Conversion_Set

friend class CSeq_loc_Conversion_Set

friend

Definition at line 297 of file seq_loc_cvt.hpp.

Member Data Documentation

m_Dst_id_Handle

CSeq_id_Handle CSeq_loc_Conversion::m_Dst_id_Handle

private

Definition at line 259 of file seq_loc_cvt.hpp.

Referenced by CombineWith(), GetDst_id_Handle(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

m_Dst_loc_Empty

CRef<CSeq_loc> CSeq_loc_Conversion::m_Dst_loc_Empty

private

Definition at line 260 of file seq_loc_cvt.hpp.

Referenced by CombineWith(), GetDstId(), GetDstLocEmpty(), GetId(), MakeDstMix(), and SetMappedLocation().

m_DstFuzz_from

CConstRef<CInt_fuzz> CSeq_loc_Conversion::m_DstFuzz_from

private

Definition at line 276 of file seq_loc_cvt.hpp.

Referenced by ConvertInterval(), ConvertPoint(), ConvertSimpleMix(), GetDstInterval(), GetDstPoint(), ResetKeepPartial(), and SetMappedLocation().

m_DstFuzz_to

CConstRef<CInt_fuzz> CSeq_loc_Conversion::m_DstFuzz_to

private

Definition at line 277 of file seq_loc_cvt.hpp.

Referenced by ConvertInterval(), ConvertPoint(), ConvertSimpleMix(), GetDstInterval(), ResetKeepPartial(), and SetMappedLocation().

m_GraphRanges

CRef<CGraphRanges> CSeq_loc_Conversion::m_GraphRanges

private

Definition at line 295 of file seq_loc_cvt.hpp.

Referenced by CSeq_loc_Conversion_Set::Convert(), Convert(), ConvertInterval(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertPacked_pnt(), ConvertPoint(), and ResetKeepPartial().

m_LastRange

TRange CSeq_loc_Conversion::m_LastRange

private

Definition at line 288 of file seq_loc_cvt.hpp.

Referenced by ConvertInterval(), ConvertPoint(), ConvertSimpleMix(), GetDstInterval(), GetDstPoint(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

m_LastStrand

ENa_strand CSeq_loc_Conversion::m_LastStrand

private

Definition at line 289 of file seq_loc_cvt.hpp.

Referenced by ConvertInterval(), ConvertPoint(), ConvertSimpleMix(), GetDstInterval(), GetDstPoint(), SetMappedLocation(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

m_LastType

EMappedObjectType CSeq_loc_Conversion::m_LastType

private

Definition at line 287 of file seq_loc_cvt.hpp.

Referenced by CheckDstInterval(), CheckDstMix(), CheckDstPoint(), Convert(), ConvertInterval(), ConvertPoint(), ConvertSimpleMix(), IsSpecialLoc(), SetDstLoc(), SetMappedLocation(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

m_Partial

bool CSeq_loc_Conversion::m_Partial

private

Definition at line 265 of file seq_loc_cvt.hpp.

Referenced by ConvertInterval(), ConvertPoint(), ConvertPos(), ConvertSimpleLoc(), GoodSrcId(), IsPartial(), Reset(), and SetMappedLocation().

m_PartialFlag

TPartialFlag CSeq_loc_Conversion::m_PartialFlag

private

Definition at line 275 of file seq_loc_cvt.hpp.

Referenced by ConvertInterval(), ConvertPoint(), ConvertSimpleMix(), GetDstInterval(), GetDstPoint(), ResetKeepPartial(), and SetMappedLocation().

m_PartialHasUnconvertedId

bool CSeq_loc_Conversion::m_PartialHasUnconvertedId

private

Definition at line 266 of file seq_loc_cvt.hpp.

Referenced by ConvertSimpleLoc(), GoodSrcId(), HasUnconvertedId(), and Reset().

m_Reverse

bool CSeq_loc_Conversion::m_Reverse

private

Definition at line 256 of file seq_loc_cvt.hpp.

Referenced by CombineWith(), ConvertInterval(), ConvertPacked_pnt(), ConvertPoint(), ConvertPos(), ConvertSimpleMix(), ConvertStrand(), CSeq_loc_Conversion(), GetDstRange(), MakeDstMix(), MinusStrand(), and SetConversion().

m_Scope

CHeapScope CSeq_loc_Conversion::m_Scope

private

Definition at line 293 of file seq_loc_cvt.hpp.

Referenced by Convert(), and ConvertSimpleLoc().

m_Shift

TSignedSeqPos CSeq_loc_Conversion::m_Shift

private

Definition at line 255 of file seq_loc_cvt.hpp.

Referenced by CombineWith(), ConvertInterval(), ConvertPoint(), ConvertPos(), ConvertSimpleMix(), CSeq_loc_Conversion(), MakeDstMix(), and SetConversion().

m_Src_from

TSeqPos CSeq_loc_Conversion::m_Src_from

private

Definition at line 251 of file seq_loc_cvt.hpp.

Referenced by CombineWith(), ConvertInterval(), ConvertSimpleMix(), CSeq_loc_Conversion(), GetDstRange(), GetSrc_from(), GetSrcRange(), CConversionRef_Less::operator()(), SetConversion(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

m_Src_id_Handle

CSeq_id_Handle CSeq_loc_Conversion::m_Src_id_Handle

private

Definition at line 250 of file seq_loc_cvt.hpp.

Referenced by CombineWith(), ConvertSimpleLoc(), GetSrc_id_Handle(), GoodSrcId(), CConversionRef_Less::operator()(), SetSrcId(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

m_Src_to

TSeqPos CSeq_loc_Conversion::m_Src_to

private

Definition at line 252 of file seq_loc_cvt.hpp.

Referenced by CombineWith(), ConvertInterval(), ConvertPoint(), ConvertPos(), ConvertSimpleMix(), CSeq_loc_Conversion(), GetDstRange(), GetSrc_to(), GetSrcRange(), CConversionRef_Less::operator()(), SetConversion(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

m_SrcLoc

CConstRef<CSeq_loc> CSeq_loc_Conversion::m_SrcLoc

private

Definition at line 290 of file seq_loc_cvt.hpp.

Referenced by ConvertSimpleMix(), and GetDstMix().

m_TotalRange

TRange CSeq_loc_Conversion::m_TotalRange

private

Definition at line 264 of file seq_loc_cvt.hpp.

Referenced by ConvertInterval(), ConvertPacked_pnt(), ConvertPoint(), ConvertSimpleMix(), GetTotalRange(), ResetKeepPartial(), and SetMappedLocation().

---

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

• include/objmgr/impl/seq_loc_cvt.hpp
• src/objmgr/seq_loc_cvt.cpp