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CHandleRangeMap Class Reference

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#include <objmgr/impl/handle_range_map.hpp>

+ Collaboration diagram for CHandleRangeMap:

Classes

struct  SAddState
 

Public Types

enum  ETransSplicing { eNoTransSplicing , eTransSplicing , eCircularRNA }
 
typedef CHandleRange::TRange TRange
 
typedef map< CSeq_id_Handle, CHandleRangeTLocMap
 
typedef TLocMap::const_iterator const_iterator
 

Public Member Functions

 CHandleRangeMap (void)
 
 ~CHandleRangeMap (void)
 
void AddLocation (const CSeq_loc &loc, ETransSplicing trans_splcing=eNoTransSplicing)
 
void AddLocation (const CSeq_loc &loc, SAddState &state)
 
void AddRange (const CSeq_id_Handle &h, const TRange &range, ENa_strand strand)
 
void AddRanges (const CSeq_id_Handle &h, const CHandleRange &hr)
 
CHandleRangeAddRanges (const CSeq_id_Handle &h)
 
const TLocMapGetMap (void) const
 
bool empty (void) const
 
void clear (void)
 
const_iterator begin (void) const
 
const_iterator find (const CSeq_id_Handle &idh) const
 
const_iterator end (void) const
 
bool IntersectingWithLoc (const CSeq_loc &loc) const
 
bool IntersectingWithMap (const CHandleRangeMap &rmap) const
 
bool TotalRangeIntersectingWith (const CHandleRangeMap &rmap) const
 
void AddRange (const CSeq_id &id, TSeqPos from, TSeqPos to, ENa_strand strand=eNa_strand_unknown)
 
void AddRange (const CSeq_id &id, const TRange &range, ENa_strand strand=eNa_strand_unknown)
 
void AddRange (const CSeq_id_Handle &h, const TRange &range, ENa_strand strand, SAddState &state)
 
void AddRange (const CSeq_id &id, const TRange &range, ENa_strand strand, SAddState &state)
 
void AddRange (const CSeq_id &id, TSeqPos from, TSeqPos to, ENa_strand strand, SAddState &state)
 
void SetMasterSeq (const CMasterSeqSegments *master_seq)
 

Private Member Functions

void x_ProcessLocation (const CSeq_loc &loc)
 

Private Attributes

TLocMap m_LocMap
 
CConstRef< CMasterSeqSegmentsm_MasterSeq
 

Detailed Description

Definition at line 87 of file handle_range_map.hpp.

Member Typedef Documentation

◆ const_iterator

Definition at line 92 of file handle_range_map.hpp.

◆ TLocMap

Definition at line 91 of file handle_range_map.hpp.

◆ TRange

Definition at line 90 of file handle_range_map.hpp.

Member Enumeration Documentation

◆ ETransSplicing

Enumerator
eNoTransSplicing 
eTransSplicing 
eCircularRNA 

Definition at line 97 of file handle_range_map.hpp.

Constructor & Destructor Documentation

◆ CHandleRangeMap()

CHandleRangeMap::CHandleRangeMap ( void  )

Definition at line 56 of file handle_range_map.cpp.

◆ ~CHandleRangeMap()

CHandleRangeMap::~CHandleRangeMap ( void  )

Definition at line 61 of file handle_range_map.cpp.

Member Function Documentation

◆ AddLocation() [1/2]

void CHandleRangeMap::AddLocation ( const CSeq_loc loc,
ETransSplicing  trans_splcing = eNoTransSplicing 
)

◆ AddLocation() [2/2]

void CHandleRangeMap::AddLocation ( const CSeq_loc loc,
SAddState state 
)

◆ AddRange() [1/6]

void CHandleRangeMap::AddRange ( const CSeq_id id,
const TRange range,
ENa_strand  strand,
SAddState state 
)

◆ AddRange() [2/6]

void CHandleRangeMap::AddRange ( const CSeq_id id,
const TRange range,
ENa_strand  strand = eNa_strand_unknown 
)

Definition at line 220 of file handle_range_map.cpp.

References AddRange(), eNoTransSplicing, and compile_time_bits::range().

◆ AddRange() [3/6]

void CHandleRangeMap::AddRange ( const CSeq_id id,
TSeqPos  from,
TSeqPos  to,
ENa_strand  strand,
SAddState state 
)

Definition at line 229 of file handle_range_map.cpp.

References AddRange().

◆ AddRange() [4/6]

void CHandleRangeMap::AddRange ( const CSeq_id id,
TSeqPos  from,
TSeqPos  to,
ENa_strand  strand = eNa_strand_unknown 
)

Definition at line 237 of file handle_range_map.cpp.

References AddRange(), and eNoTransSplicing.

◆ AddRange() [5/6]

void CHandleRangeMap::AddRange ( const CSeq_id_Handle h,
const TRange range,
ENa_strand  strand 
)

◆ AddRange() [6/6]

void CHandleRangeMap::AddRange ( const CSeq_id_Handle h,
const TRange range,
ENa_strand  strand,
SAddState state 
)

◆ AddRanges() [1/2]

CHandleRange & CHandleRangeMap::AddRanges ( const CSeq_id_Handle h)

Definition at line 300 of file handle_range_map.cpp.

References m_LocMap.

◆ AddRanges() [2/2]

void CHandleRangeMap::AddRanges ( const CSeq_id_Handle h,
const CHandleRange hr 
)

◆ begin()

const_iterator CHandleRangeMap::begin ( void  ) const
inline

Definition at line 122 of file handle_range_map.hpp.

References map_checker< Container >::begin(), and m_LocMap.

Referenced by CSeq_annot_Finder::x_Find().

◆ clear()

void CHandleRangeMap::clear ( void  )

Definition at line 66 of file handle_range_map.cpp.

References map_checker< Container >::clear(), and m_LocMap.

◆ empty()

bool CHandleRangeMap::empty ( void  ) const
inline

◆ end()

const_iterator CHandleRangeMap::end ( void  ) const
inline

◆ find()

const_iterator CHandleRangeMap::find ( const CSeq_id_Handle idh) const
inline

Definition at line 123 of file handle_range_map.hpp.

References map_checker< Container >::find(), and m_LocMap.

Referenced by CAnnot_Collector::x_SearchTSE().

◆ GetMap()

const TLocMap& CHandleRangeMap::GetMap ( void  ) const
inline

◆ IntersectingWithLoc()

bool CHandleRangeMap::IntersectingWithLoc ( const CSeq_loc loc) const

Definition at line 306 of file handle_range_map.cpp.

References AddLocation(), and IntersectingWithMap().

◆ IntersectingWithMap()

bool CHandleRangeMap::IntersectingWithMap ( const CHandleRangeMap rmap) const

◆ SetMasterSeq()

void CHandleRangeMap::SetMasterSeq ( const CMasterSeqSegments master_seq)
inline

Definition at line 147 of file handle_range_map.hpp.

References m_MasterSeq.

Referenced by CSeqsRange::Add(), and CSeq_annot_Info::x_InitFeatTableKeys().

◆ TotalRangeIntersectingWith()

bool CHandleRangeMap::TotalRangeIntersectingWith ( const CHandleRangeMap rmap) const

◆ x_ProcessLocation()

void CHandleRangeMap::x_ProcessLocation ( const CSeq_loc loc)
private

Member Data Documentation

◆ m_LocMap

TLocMap CHandleRangeMap::m_LocMap
private

◆ m_MasterSeq

CConstRef<CMasterSeqSegments> CHandleRangeMap::m_MasterSeq
private

Definition at line 156 of file handle_range_map.hpp.

Referenced by AddRange(), and SetMasterSeq().


The documentation for this class was generated from the following files:
Modified on Fri Dec 01 04:43:38 2023 by modify_doxy.py rev. 669887