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NCBI C++ ToolKit: src/objmgr/util/seq_loc_util.cpp File Reference

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TSeqPos  GetLength (const CSeq_id &id, CScope *scope)   Get sequence length if scope not null, else return max possible TSeqPos. More...
  TSeqPos  GetLength (const CSeq_loc &loc, CScope *scope)   Get length of sequence represented by CSeq_loc, if possible. More...
  TSeqPos  GetCoverage (const CSeq_loc &loc, CScope *scope)   Get number of unique bases in the location. More...
  TSeqPos  GetLength (const CSeq_loc_mix &mix, CScope *scope)   Get length of CSeq_loc_mix == sum (length of embedded CSeq_locs) More...
  bool  IsValid (const CSeq_point &pt, CScope *scope)   Checks that point >= 0 and point < length of Bioseq. More...
  bool  IsValid (const CPacked_seqpnt &pts, CScope *scope)   Checks that all points >=0 and < length of CBioseq. More...
  bool  IsValid (const CSeq_interval &interval, CScope *scope)   Checks from and to of CSeq_interval. More...
  bool  IsSameBioseq (const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag)   Determines if two CSeq_ids represent the same CBioseq. More...
  bool  IsSameBioseq (const CSeq_id_Handle &id1, const CSeq_id_Handle &id2, CScope *scope, CScope::EGetBioseqFlag get_flag)   static const CSeq_id *  s_GetId (const CSeq_loc &loc, CScope *scope, string *msg=NULL)   const CSeq_id &  GetId (const CSeq_loc &loc, CScope *scope)   If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found, else throws CObjmgrUtilException exception. More...
  CSeq_id_Handle  GetIdHandle (const CSeq_loc &loc, CScope *scope)   bool  IsOneBioseq (const CSeq_loc &loc, CScope *scope)   Returns true if all embedded CSeq_ids represent the same CBioseq, else false. More...
  static ENa_strand  s_GetStrand (const CSeq_loc &loc)   ENa_strand  GetStrand (const CSeq_loc &loc, CScope *scope)   Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in same loc Returns eNa_strand_both if loc is a Whole Returns strand otherwise. More...
  TSeqPos  GetStart (const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext)   If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location. More...
  TSeqPos  GetStop (const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext)   If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location. More...
  void  ChangeSeqId (CSeq_id *id, bool best, CScope *scope)   Change a CSeq_id to the one for the CBioseq that it represents that has the best rank or worst rank according on value of best. More...
  void  ChangeSeqLocId (CSeq_loc *loc, bool best, CScope *scope)   Change each of the CSeq_ids embedded in a CSeq_loc to the best or worst CSeq_id accoring to the value of best. More...
  bool  BadSeqLocSortOrder (const CBioseq_Handle &bsh, const CSeq_loc &loc)   Returns true if the order of Seq_locs is bad, otherwise, false. More...
  bool  BadSeqLocSortOrder (const CBioseq &seq, const CSeq_loc &loc, CScope *scope)   ESeqLocCheck  SeqLocCheck (const CSeq_loc &loc, CScope *scope)   Checks that a CSeq_loc is all on one strand on one CBioseq. More...
  TSeqPos  LocationOffset (const CSeq_loc &outer, const CSeq_loc &inner, EOffsetType how, CScope *scope)   returns (TSeqPos)-1 if the locations don't overlap More...
  void  SeqIntPartialCheck (const CSeq_interval &itv, unsigned int &retval, bool is_first, bool is_last, CScope &scope)   int  SeqLocPartialCheck (const CSeq_loc &loc, CScope *scope)   CSeq_loc *  SeqLocRevCmpl (const CSeq_loc &loc, CScope *)   Get reverse complement of the seq-loc (?) More...
  CSeq_id_Handle  s_GetSynHandle (CSeq_id_Handle id, TSynMap &syns, CScope *scope)   void  s_SeqLocToRangeInfoMap (const CSeq_loc &loc, TRangeInfoMap &infos, TSynMap &syns, CScope *scope)   ECompare  s_CompareOverlapping (const CSeq_loc &me, const CSeq_loc &you, TSynMap &syns, CScope *scope)   bool  s_CheckAbutting (const CSeq_loc &loc1, const CSeq_loc &loc2, TSynMap &syns, CScope *scope, ESeqLocExtremes ext)   ECompare  Compare (const CSeq_loc &me, const CSeq_loc &you, CScope *scope)   Returns the sequence::ECompare containment relationship between CSeq_locs. More...
  ECompare  Compare (const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope, TCompareFlags flags)   Compare the seq-locs. More...
  bool  s_Test_Strands (ENa_strand strand1, ENa_strand strand2)   Int8  AbsInt8 (Int8 x)   void  s_SeqLocToTotalRangeInfoMap (const CSeq_loc &loc, TTotalRangeInfoMap &infos, TSynMap &syns, CScope *scope)   int  TestForOverlap (const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len, CScope *scope)   Calls TestForOverlap64() and if the result is greater than kMax_Int truncates it to kMax_Int. More...
  void  s_SeqLocToRangeInfoMapByStrand (const CSeq_loc &loc, TRangeInfoMapByStrand &infos, TSynMap &syns, CScope *scope)   STopologyInfo  s_GetTopology (CSeq_id_Handle idh, TTopologyMap &topologies, TOverlapFlags flags, CScope *scope)   void  s_SeqLocToTotalRangesInfoMapByStrand (const CSeq_loc &loc, TRangeInfoMapByStrand &infos, TSynMap &syns, TTopologyMap &topologies, TOverlapFlags flags, CScope *scope)   Int8  s_GetUncoveredLength (const TRangeInfoList &ranges1, const TRangeInfoList &ranges2)   Int8  s_GetUncoveredLength (const TRangeInfoMapByStrand &ranges1, const TRangeInfoMapByStrand &ranges2)   bool  s_Test_Subset (const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)   bool  s_Test_CheckIntervals (CSeq_loc_CI it1, CSeq_loc_CI it2, bool minus_strand, CScope *scope, bool single_id)   Int8  s_Test_Extremes (const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSynMap &syns, TTopologyMap &topologies, TOverlapFlags flags, CScope *scope)   Int8  s_Test_Interval (const CSeq_loc &loc1, const CSeq_loc &loc2, TSynMap &syns, TTopologyMap &topologies, TOverlapFlags flags, CScope *scope)   Int8  s_TestForOverlapEx (const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TOverlapFlags flags, TSeqPos circular_len, CScope *scope)   Int8  TestForOverlap64 (const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len, CScope *scope)   64-bit version of TestForOverlap() Check if the two locations have ovarlap of a given type. More...
  Int8  TestForOverlapEx (const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, CScope *scope, TOverlapFlags flags)   Updated version of TestForOverlap64(). More...
  CRef< CSeq_loc >  Seq_loc_Merge (const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)   Merge ranges in the seq-loc. More...
  CRef< CSeq_loc >  Seq_loc_Add (const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)   Add two seq-locs. More...
  CRef< CSeq_loc >  Seq_loc_Subtract (const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)   Subtract the second seq-loc from the first one. More...
  ◆ NCBI_USE_ERRCODE_X ◆ TRangeInfo ◆ TRangeInfoByStrand ◆ TRangeInfoList ◆ TRangeInfoListByStrand ◆ TRangeInfoMap ◆ TRangeInfoMapByStrand ◆ TSynMap ◆ TTopologyMap ◆ TTotalRangeInfoMap ◆ AbsInt8() ◆ s_CheckAbutting()

Definition at line 1153 of file seq_loc_util.cpp.

References CSeq_loc_CI::eEmpty_Allow, eExtreme_Positional, CSeq_loc_CI::eOrder_Biological, CSeq_loc_CI::eOrder_Positional, CRange_Base::GetFrom(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id_Handle(), CSeq_loc_CI::GetSize(), CSeq_loc_CI::GetStrand(), COpenRange< Position >::GetToOpen(), CSeq_loc_CI::IsEmpty(), IsReverse(), CSeq_loc_CI::IsWhole(), s_GetSynHandle(), and CSeq_loc_CI::SetPos().

Referenced by Compare().

◆ s_CompareOverlapping()

Definition at line 1036 of file seq_loc_util.cpp.

References _ASSERT, map_checker< Container >::begin(), eContained, eContains, map_checker< Container >::end(), eNoOverlap, eOverlap, eSame, map_checker< Container >::find(), ITERATE, s_SeqLocToRangeInfoMap(), and map_checker< Container >::size().

Referenced by Compare().

◆ s_GetId() ◆ s_GetStrand()

Definition at line 393 of file seq_loc_util.cpp.

References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, eNa_strand_both, eNa_strand_other, eNa_strand_plus, eNa_strand_unknown, CPacked_seqint_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_bond_Base::GetA(), CSeq_bond_Base::GetB(), CSeq_loc_Base::GetBond(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), GetStrand(), CPacked_seqpnt_Base::GetStrand(), CSeq_interval_Base::GetStrand(), CSeq_point_Base::GetStrand(), i, CSeq_bond_Base::IsSetB(), CPacked_seqpnt_Base::IsSetStrand(), CSeq_interval_Base::IsSetStrand(), CSeq_point_Base::IsSetStrand(), ITERATE, and CSeq_loc_Base::Which().

Referenced by GetStrand().

◆ s_GetSynHandle() ◆ s_GetTopology()

Definition at line 1356 of file seq_loc_util.cpp.

References map_checker< Container >::end(), CSeq_inst_Base::eTopology_circular, map_checker< Container >::find(), flags, fOverlap_IgnoreTopology, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetInst_Topology(), info, CBioseq_Handle::IsSetInst_Topology(), and kInvalidSeqPos.

Referenced by s_SeqLocToTotalRangesInfoMapByStrand().

◆ s_GetUncoveredLength() [1/2]

Definition at line 1479 of file seq_loc_util.cpp.

References COpenRange< TSeqPos >::GetEmpty(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), COpenRange< Position >::IntersectingWith(), COpenRange< Position >::IsWhole(), ITERATE, max(), and CRange_Base::SetFrom().

Referenced by s_GetUncoveredLength(), s_Test_Extremes(), and s_Test_Interval().

◆ s_GetUncoveredLength() [2/2] ◆ s_SeqLocToRangeInfoMap()

Definition at line 1012 of file seq_loc_util.cpp.

References CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Positional, CRange_Base::GetFrom(), GetLength(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSeq_id_Handle(), COpenRange< Position >::GetToOpen(), info, CSeq_loc_CI::IsWhole(), NON_CONST_ITERATE, and s_GetSynHandle().

Referenced by s_CompareOverlapping().

◆ s_SeqLocToRangeInfoMapByStrand()

Definition at line 1318 of file seq_loc_util.cpp.

References CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Positional, CRange_Base::GetFrom(), GetLength(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSeq_id_Handle(), CSeq_loc_CI::GetStrand(), COpenRange< Position >::GetToOpen(), info, IsReverse(), CSeq_loc_CI::IsSetStrand(), CSeq_loc_CI::IsWhole(), NON_CONST_ITERATE, and s_GetSynHandle().

Referenced by s_Test_Interval(), and s_Test_Subset().

◆ s_SeqLocToTotalRangeInfoMap()

Definition at line 1276 of file seq_loc_util.cpp.

References CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Positional, CRange_Base::GetFrom(), GetLength(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSeq_id_Handle(), CSeq_loc_CI::GetStrand(), COpenRange< Position >::GetToOpen(), IsReverse(), CSeq_loc_CI::IsWhole(), s_GetSynHandle(), and COpenRange< Position >::SetOpen().

◆ s_SeqLocToTotalRangesInfoMapByStrand()

Definition at line 1385 of file seq_loc_util.cpp.

References STopologyInfo::circular, COpenRange< Position >::CombineWith(), CSeq_loc_CI::eEmpty_Skip, COpenRange< Position >::Empty(), CSeq_loc_CI::eOrder_Biological, flags, COpenRange< TSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id_Handle(), CSeq_loc_CI::GetStrand(), COpenRange< TSeqPos >::GetWholeToOpen(), info, IsReverse(), CSeq_loc_CI::IsSetStrand(), kInvalidSeqPos, STopologyInfo::length, NON_CONST_ITERATE, s_GetSynHandle(), s_GetTopology(), CRange_Base::SetFrom(), and COpenRange< Position >::SetToOpen().

Referenced by s_Test_Extremes(), and s_Test_Interval().

◆ s_Test_CheckIntervals() ◆ s_Test_Extremes() ◆ s_Test_Interval() ◆ s_Test_Strands() ◆ s_Test_Subset() ◆ s_TestForOverlapEx()

Definition at line 1815 of file seq_loc_util.cpp.

References STopologyInfo::circular, eNa_strand_minus, eNa_strand_other, eOverlap_CheckIntervals, eOverlap_CheckIntRev, eOverlap_Contained, eOverlap_Contains, eOverlap_Interval, eOverlap_Simple, eOverlap_Subset, eOverlap_SubsetRev, flags, fOverlap_IgnoreTopology, fOverlap_NoMultiSeq, fOverlap_NoMultiStrand, GetCoverage(), CRange_Base::GetFrom(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), GetLength(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id(), GetStrand(), CSeq_loc_CI::GetStrand(), CRange_Base::GetTo(), IsSameBioseq(), kInvalidSeqPos, STopologyInfo::length, NCBI_THROW, NULL, s_Test_CheckIntervals(), s_Test_Extremes(), s_Test_Interval(), s_Test_Strands(), s_Test_Subset(), and swap().

Referenced by TestForOverlap64(), and TestForOverlapEx().

◆ SeqIntPartialCheck()

Definition at line 713 of file seq_loc_util.cpp.

References CInt_fuzz_Base::e_Lim, CInt_fuzz_Base::e_Range, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_unk, eNa_strand_minus, eSeqlocPartial_Internal, eSeqlocPartial_Limwrong, eSeqlocPartial_Nointernal, eSeqlocPartial_Nostart, eSeqlocPartial_Nostop, eSeqlocPartial_Start, eSeqlocPartial_Stop, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CInt_fuzz_Base::GetLim(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CInt_fuzz_Base::IsLim(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetStrand(), and CInt_fuzz_Base::Which().

Referenced by SeqLocPartialCheck().

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