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NCBI C++ ToolKit: include/objmgr/impl/seq_loc_cvt.hpp Source File

1 #ifndef SEQ_LOC_CVT__HPP 2 #define SEQ_LOC_CVT__HPP 104  bool

GoodSrcId(

const CSeq_id

&

id

);

142

EConvertFlag flag = eCnvDefault);

145  void

ResetKeepPartial(

void

);

153  return

m_PartialHasUnconvertedId;

158

m_Src_id_Handle = src;

164  return

m_Src_id_Handle;

187  return

m_Dst_id_Handle;

191  return

m_Dst_loc_Empty->GetEmpty();

206  void

CheckDstInterval(

void

);

207  void

CheckDstPoint(

void

);

208  void

CheckDstMix(

void

);

216  bool

IsSpecialLoc(

void

)

const

;

220  return

*m_Dst_loc_Empty;

224  return

m_Dst_loc_Empty->SetEmpty();

230  TRange

(ConvertPos(m_Src_to), ConvertPos(m_Src_from)) :

231  TRange

(ConvertPos(m_Src_from), ConvertPos(m_Src_to));

235  return TRange

(m_Src_from, m_Src_to);

240  bool

ConvertSimpleMix(

const CSeq_loc

& src);

242

EConvertFlag flag = eCnvDefault);

270

fPartial_from = 1 << 0,

285

eMappedObjType_Seq_loc_mix

326  unsigned int

loc_index);

331  unsigned int

loc_index);

341  return

m_PartialHasUnconvertedId;

347  return

m_Dst_id_Handles;

357  unsigned int

loc_index);

360  unsigned int

loc_index);

362  bool

ConvertPacked_int(

const CSeq_loc

& src,

364  unsigned int

loc_index);

365  bool

ConvertPacked_pnt(

const CSeq_loc

& src,

367  unsigned int

loc_index);

368  bool

ConvertMix(

const CSeq_loc

& src,

370  unsigned int

loc_index);

371  bool

ConvertEquiv(

const CSeq_loc

& src,

373  unsigned int

loc_index);

374  bool

ConvertBond(

const CSeq_loc

& src,

376  unsigned int

loc_index);

410  if

( src_pos < m_Src_from || src_pos >

m_Src_to

) {

ENa_strand Reverse(ENa_strand s)

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

namespace ncbi::objects::

unsigned int m_SingleIndex

set< CSeq_id_Handle > TSeq_id_Handles

TSeq_id_Handles m_Dst_id_Handles

TConvByIndex m_CvtByIndex

const TSeq_id_Handles & GetDst_id_Handles(void) const

CRangeMultimap< CRef< CSeq_loc_Conversion >, TSeqPos > TRangeMap

map< CSeq_id_Handle, TRangeMap > TIdMap

bool HasUnconvertedId(void) const

CRef< CGraphRanges > m_GraphRanges

bool m_PartialHasUnconvertedId

map< unsigned int, TIdMap > TConvByIndex

TRangeMap::iterator TRangeIterator

CRef< CSeq_loc_Conversion > m_SingleConv

bool IsPartial(void) const

bool m_PartialHasUnconvertedId

CSeq_id_Handle m_Src_id_Handle

bool HasUnconvertedId(void) const

bool IsPartial(void) const

CConstRef< CInt_fuzz > m_DstFuzz_to

CRef< CSeq_loc > m_Dst_loc_Empty

const TRange & GetTotalRange(void) const

TSeqPos GetSrc_from(void) const

@ eMappedObjType_Seq_point

@ eMappedObjType_Seq_interval

const CSeq_id & GetId(void) const

bool GoodSrcId(const CSeq_id &id)

EMappedObjectType m_LastType

ENa_strand ConvertStrand(ENa_strand strand) const

bool IsSpecialLoc(void) const

CSeq_id_Handle m_Dst_id_Handle

TPartialFlag m_PartialFlag

CSeq_loc & GetDstLocEmpty(void)

CConstRef< CInt_fuzz > m_DstFuzz_from

TSeqPos GetSrc_to(void) const

bool MinusStrand(void) const

TRange GetSrcRange(void) const

TSeqPos ConvertPos(TSeqPos src_pos)

CConstRef< CSeq_loc > m_SrcLoc

const CSeq_id_Handle & GetDst_id_Handle(void) const

const CSeq_id_Handle & GetSrc_id_Handle(void) const

CRef< CGraphRanges > m_GraphRanges

void SetSrcId(const CSeq_id_Handle &src)

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJMGR_EXPORT

ENa_strand

strand of nucleic acid

list< CRef< CSeq_loc > > Tdata

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

const value_slice::CValueConvert< value_slice::SRunTimeCP, FROM > Convert(const FROM &value)

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