CHandleRange Class Reference

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#include <objmgr/impl/handle_range.hpp>

Collaboration diagram for CHandleRange:

Public Types
enum	ETotalRangeFlags { eStrandPlus = 1 << 0 , eStrandMinus = 1 << 1 , eStrandAny = eStrandPlus | eStrandMinus }
typedef CRange< TSeqPos >	TRange
typedef COpenRange< TSeqPos >	TOpenRange
typedef pair< TRange, ENa_strand >	TRangeWithStrand
typedef vector< TRangeWithStrand >	TRanges
typedef TRanges::const_iterator	const_iterator
typedef unsigned int	TTotalRangeFlags

Public Member Functions
	CHandleRange (void)
	CHandleRange (const CHandleRange &src, const TOpenRange &range)
	Trim src with filter range. More...
	~CHandleRange (void)
bool	Empty (void) const
const_iterator	begin (void) const
const_iterator	end (void) const
void	AddRange (TRange range, ENa_strand strand)
void	AddRange (TRange range, ENa_strand strand, bool more_before, bool more_after, bool circular_rna=false)
void	MergeRange (TRange range, ENa_strand strand)
void	AddRanges (const CHandleRange &hr)
bool	HasGaps (void) const
bool	IsMultipart (void) const
bool	IsCircular (void) const
bool	IsSingleStrand (void) const
TTotalRangeFlags	GetStrandsFlag (void) const
TRange	GetOverlappingRange (TTotalRangeFlags flags=eStrandAny) const
TSeqPos	GetLeft (void) const
TSeqPos	GetRight (void) const
TRange	GetCircularRangeStart (bool include_origin=true) const
TRange	GetCircularRangeEnd (bool include_origin=true) const
TRange	GetOverlappingRange (const TRange &range) const
bool	IntersectingWith (const CHandleRange &hr) const
bool	IntersectingWithTotalRange (const CHandleRange &hr) const
bool	IntersectingWithSubranges (const CHandleRange &hr) const
bool	IntersectingWith_NoStrand (const CHandleRange &hr) const
bool	IntersectingWith (const TRange &range, ENa_strand strand=eNa_strand_unknown) const

Private Member Functions
bool	x_IncludesPlus (const ENa_strand &strand) const
bool	x_IncludesMinus (const ENa_strand &strand) const

Static Private Member Functions
static bool	x_IntersectingStrands (ENa_strand str1, ENa_strand str2)

Private Attributes
TRanges	m_Ranges
TRange	m_TotalRanges_plus
TRange	m_TotalRanges_minus
bool	m_IsCircular
bool	m_IsSingleStrand
bool	m_MoreBefore
bool	m_MoreAfter

Friends
class	CHandleRangeMap

Detailed Description

Definition at line 44 of file handle_range.hpp.

Member Typedef Documentation

const_iterator

typedef TRanges::const_iterator CHandleRange::const_iterator

Definition at line 51 of file handle_range.hpp.

TOpenRange

typedef COpenRange<TSeqPos> CHandleRange::TOpenRange

Definition at line 48 of file handle_range.hpp.

TRange

typedef CRange<TSeqPos> CHandleRange::TRange

Definition at line 47 of file handle_range.hpp.

TRanges

typedef vector<TRangeWithStrand> CHandleRange::TRanges

Definition at line 50 of file handle_range.hpp.

TRangeWithStrand

typedef pair<TRange, ENa_strand> CHandleRange::TRangeWithStrand

Definition at line 49 of file handle_range.hpp.

TTotalRangeFlags

typedef unsigned int CHandleRange::TTotalRangeFlags

Definition at line 84 of file handle_range.hpp.

Member Enumeration Documentation

ETotalRangeFlags

enum CHandleRange::ETotalRangeFlags

Enumerator
eStrandPlus
eStrandMinus
eStrandAny

Definition at line 79 of file handle_range.hpp.

Constructor & Destructor Documentation

CHandleRange() [1/2]

CHandleRange::CHandleRange

(

void

)

Definition at line 49 of file handle_range.cpp.

CHandleRange() [2/2]

CHandleRange::CHandleRange	(	const CHandleRange &	src,
		const TOpenRange &	range
	)

Trim src with filter range.

Definition at line 60 of file handle_range.cpp.

References AddRange(), and ITERATE.

~CHandleRange()

CHandleRange::~CHandleRange

(

void

)

Definition at line 76 of file handle_range.cpp.

Member Function Documentation

AddRange() [1/2]

void CHandleRange::AddRange	(	TRange	range,
		ENa_strand	strand
	)

Definition at line 109 of file handle_range.cpp.

References compile_time_bits::range().

Referenced by CHandleRangeMap::AddRange(), AddRanges(), CHandleRange(), MergeRange(), CAnnot_Collector::x_CollectMapped(), CAnnot_Collector::x_Initialize(), and CAnnot_Collector::x_SearchMapped().

AddRange() [2/2]

void CHandleRange::AddRange	(	TRange	range,
		ENa_strand	strand,
		bool	more_before,
		bool	more_after,
		bool	circular_rna = false
	)

Definition at line 115 of file handle_range.cpp.

References _ASSERT, COpenRange< Position >::Empty(), COpenRange< TSeqPos >::GetEmpty(), m_IsCircular, m_IsSingleStrand, m_MoreAfter, m_MoreBefore, m_Ranges, m_TotalRanges_minus, m_TotalRanges_plus, NON_CONST_REVERSE_ITERATE, compile_time_bits::range(), x_IncludesMinus(), and x_IncludesPlus().

AddRanges()

void CHandleRange::AddRanges

(

const CHandleRange &

hr

)

Definition at line 211 of file handle_range.cpp.

References AddRange(), and ITERATE.

begin()

CHandleRange::const_iterator CHandleRange::begin ( void  ) const

inline

Definition at line 150 of file handle_range.hpp.

References m_Ranges.

Referenced by CAnnot_Collector::x_CollectSegments(), CAnnot_Collector::x_SearchRange(), and CAnnot_Collector::x_SearchSegments().

Empty()

bool CHandleRange::Empty ( void  ) const

inline

Definition at line 143 of file handle_range.hpp.

References m_Ranges.

Referenced by CAnnot_Collector::x_CollectMapped(), CAnnot_Collector::x_SearchMapped(), and CAnnot_Collector::x_SearchTSE().

end()

CHandleRange::const_iterator CHandleRange::end ( void  ) const

inline

Definition at line 157 of file handle_range.hpp.

References m_Ranges.

Referenced by CAnnot_Collector::x_SearchRange().

GetCircularRangeEnd()

CHandleRange::TRange CHandleRange::GetCircularRangeEnd

(

bool

include_origin = true

)

const

Definition at line 398 of file handle_range.cpp.

References _ASSERT, COpenRange< TSeqPos >::GetWholeFrom(), COpenRange< TSeqPos >::GetWholeTo(), IsReverse(), m_IsCircular, m_Ranges, m_TotalRanges_minus, CRange_Base::SetFrom(), and CRange_Base::SetTo().

Referenced by CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatTableKeys(), and CSeq_annot_Info::x_MapAnnotObject().

GetCircularRangeStart()

CHandleRange::TRange CHandleRange::GetCircularRangeStart

(

bool

include_origin = true

)

const

Definition at line 378 of file handle_range.cpp.

References _ASSERT, COpenRange< TSeqPos >::GetWholeFrom(), COpenRange< TSeqPos >::GetWholeTo(), IsReverse(), m_IsCircular, m_Ranges, m_TotalRanges_plus, CRange_Base::SetFrom(), and CRange_Base::SetTo().

Referenced by CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatTableKeys(), and CSeq_annot_Info::x_MapAnnotObject().

GetLeft()

TSeqPos CHandleRange::GetLeft

(

void

)

const

Definition at line 299 of file handle_range.cpp.

References CRange_Base::GetFrom(), IsReverse(), m_IsCircular, m_Ranges, m_TotalRanges_minus, m_TotalRanges_plus, and min().

GetOverlappingRange() [1/2]

CHandleRange::TRange CHandleRange::GetOverlappingRange

(

const TRange &

range

)

const

Definition at line 418 of file handle_range.cpp.

References COpenRange< TSeqPos >::GetEmpty(), COpenRange< Position >::IntersectionWith(), ITERATE, m_Ranges, and compile_time_bits::range().

GetOverlappingRange() [2/2]

CHandleRange::TRange CHandleRange::GetOverlappingRange

(

TTotalRangeFlags

flags = eStrandAny

)

const

Definition at line 331 of file handle_range.cpp.

References _ASSERT, eStrandMinus, eStrandPlus, flags, COpenRange< TSeqPos >::GetEmpty(), COpenRange< TSeqPos >::GetWhole(), COpenRange< TSeqPos >::GetWholeFrom(), COpenRange< TSeqPos >::GetWholeTo(), IsReverse(), m_IsCircular, m_IsSingleStrand, m_MoreAfter, m_MoreBefore, m_Ranges, m_TotalRanges_minus, m_TotalRanges_plus, CRange_Base::SetFrom(), CRange_Base::SetTo(), x_IncludesMinus(), and x_IncludesPlus().

Referenced by COneSeqRange::Add(), IntersectingWith_NoStrand(), CSeq_annot_Info::x_AddAlignIndex(), CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeq_annot_Info::x_InitGraphKeys(), CSeq_annot_Info::x_InitLocsKeys(), CSeq_annot_Info::x_MapAnnotObject(), CAnnot_Collector::x_SearchObjects(), CAnnot_Collector::x_SearchRange(), and CAnnot_Collector::x_SearchTSE().

GetRight()

TSeqPos CHandleRange::GetRight

(

void

)

const

Definition at line 311 of file handle_range.cpp.

References COpenRange< Position >::Empty(), CRange_Base::GetTo(), IsReverse(), m_IsCircular, m_Ranges, m_TotalRanges_minus, m_TotalRanges_plus, and max().

GetStrandsFlag()

CHandleRange::TTotalRangeFlags CHandleRange::GetStrandsFlag

(

void

)

const

Definition at line 81 of file handle_range.cpp.

References COpenRange< Position >::Empty(), eStrandMinus, eStrandPlus, m_IsCircular, m_Ranges, m_TotalRanges_minus, m_TotalRanges_plus, x_IncludesMinus(), and x_IncludesPlus().

Referenced by CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeq_annot_Info::x_MapAnnotObject(), and CAnnot_Collector::x_MatchRange().

HasGaps()

bool CHandleRange::HasGaps

(

void

)

const

Definition at line 445 of file handle_range.cpp.

References m_MoreAfter, m_MoreBefore, and m_Ranges.

Referenced by CSeq_annot_Info::x_AddAlignIndex(), CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeq_annot_Info::x_InitGraphKeys(), CSeq_annot_Info::x_InitLocsKeys(), and CSeq_annot_Info::x_MapAnnotObject().

IntersectingWith() [1/2]

bool CHandleRange::IntersectingWith

(

const CHandleRange &

hr

)

const

Definition at line 254 of file handle_range.cpp.

References IntersectingWithSubranges(), and IntersectingWithTotalRange().

Referenced by IntersectingWith_NoStrand(), and CAnnot_Collector::x_MatchRange().

IntersectingWith() [2/2]

bool CHandleRange::IntersectingWith	(	const TRange &	range,
		ENa_strand	strand = eNa_strand_unknown
	)		const

Definition at line 430 of file handle_range.cpp.

References ITERATE, m_Ranges, compile_time_bits::range(), and x_IntersectingStrands().

IntersectingWith_NoStrand()

bool CHandleRange::IntersectingWith_NoStrand

(

const CHandleRange &

hr

)

const

Definition at line 260 of file handle_range.cpp.

References GetOverlappingRange(), IntersectingWith(), ITERATE, and m_Ranges.

Referenced by CAnnot_Collector::x_MatchRange().

IntersectingWithSubranges()

bool CHandleRange::IntersectingWithSubranges

(

const CHandleRange &

hr

)

const

Definition at line 239 of file handle_range.cpp.

References ITERATE, m_Ranges, and x_IntersectingStrands().

Referenced by IntersectingWith().

IntersectingWithTotalRange()

bool CHandleRange::IntersectingWithTotalRange

(

const CHandleRange &

hr

)

const

Definition at line 231 of file handle_range.cpp.

References COpenRange< Position >::IntersectingWith(), IsCircular(), m_TotalRanges_minus, and m_TotalRanges_plus.

Referenced by IntersectingWith(), and CAnnot_Collector::x_SearchTSE().

IsCircular()

bool CHandleRange::IsCircular ( void  ) const

inline

Definition at line 171 of file handle_range.hpp.

References m_IsCircular.

Referenced by IntersectingWithTotalRange(), CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatTableKeys(), and CSeq_annot_Info::x_MapAnnotObject().

IsMultipart()

bool CHandleRange::IsMultipart ( void  ) const

inline

Definition at line 164 of file handle_range.hpp.

References m_IsCircular, and m_IsSingleStrand.

IsSingleStrand()

bool CHandleRange::IsSingleStrand ( void  ) const

inline

Definition at line 178 of file handle_range.hpp.

References m_IsSingleStrand.

MergeRange()

void CHandleRange::MergeRange	(	TRange	range,
		ENa_strand	strand
	)

Definition at line 276 of file handle_range.cpp.

References AddRange(), eNa_strand_unknown, m_Ranges, and compile_time_bits::range().

x_IncludesMinus()

bool CHandleRange::x_IncludesMinus ( const ENa_strand &  strand ) const

inlineprivate

Definition at line 193 of file handle_range.hpp.

References eNa_strand_both, eNa_strand_both_rev, eNa_strand_minus, and eNa_strand_unknown.

Referenced by AddRange(), GetOverlappingRange(), and GetStrandsFlag().

x_IncludesPlus()

bool CHandleRange::x_IncludesPlus ( const ENa_strand &  strand ) const

inlineprivate

Definition at line 185 of file handle_range.hpp.

References eNa_strand_minus.

Referenced by AddRange(), GetOverlappingRange(), and GetStrandsFlag().

x_IntersectingStrands()

bool CHandleRange::x_IntersectingStrands ( ENa_strand  str1, ENa_strand  str2  )

staticprivate

Definition at line 219 of file handle_range.cpp.

References eNa_strand_unknown.

Referenced by IntersectingWith(), and IntersectingWithSubranges().

Friends And Related Function Documentation

CHandleRangeMap

friend class CHandleRangeMap

friend

Definition at line 138 of file handle_range.hpp.

Member Data Documentation

m_IsCircular

bool CHandleRange::m_IsCircular

private

Definition at line 132 of file handle_range.hpp.

Referenced by AddRange(), GetCircularRangeEnd(), GetCircularRangeStart(), GetLeft(), GetOverlappingRange(), GetRight(), GetStrandsFlag(), IsCircular(), and IsMultipart().

m_IsSingleStrand

bool CHandleRange::m_IsSingleStrand

private

Definition at line 133 of file handle_range.hpp.

Referenced by AddRange(), GetOverlappingRange(), IsMultipart(), and IsSingleStrand().

m_MoreAfter

bool CHandleRange::m_MoreAfter

private

Definition at line 135 of file handle_range.hpp.

Referenced by AddRange(), GetOverlappingRange(), and HasGaps().

m_MoreBefore

bool CHandleRange::m_MoreBefore

private

Definition at line 134 of file handle_range.hpp.

Referenced by CHandleRangeMap::AddRange(), AddRange(), GetOverlappingRange(), and HasGaps().

m_Ranges

TRanges CHandleRange::m_Ranges

private

Definition at line 129 of file handle_range.hpp.

Referenced by AddRange(), begin(), Empty(), end(), GetCircularRangeEnd(), GetCircularRangeStart(), GetLeft(), GetOverlappingRange(), GetRight(), GetStrandsFlag(), HasGaps(), IntersectingWith(), IntersectingWith_NoStrand(), IntersectingWithSubranges(), and MergeRange().

m_TotalRanges_minus

TRange CHandleRange::m_TotalRanges_minus

private

Definition at line 131 of file handle_range.hpp.

Referenced by AddRange(), GetCircularRangeEnd(), GetLeft(), GetOverlappingRange(), GetRight(), GetStrandsFlag(), and IntersectingWithTotalRange().

m_TotalRanges_plus

TRange CHandleRange::m_TotalRanges_plus

private

Definition at line 130 of file handle_range.hpp.

Referenced by AddRange(), GetCircularRangeStart(), GetLeft(), GetOverlappingRange(), GetRight(), GetStrandsFlag(), and IntersectingWithTotalRange().

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

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