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NCBI C++ ToolKit: include/objects/seqloc/Seq_loc_mix.hpp Source File

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37 #ifndef OBJECTS_SEQLOC_SEQ_LOC_MIX_HPP 38 #define OBJECTS_SEQLOC_SEQ_LOC_MIX_HPP 90  void

AddSeqLoc(

const CSeq_loc

& other);

98  bool

IsReverseStrand(

void

)

const

;

108  const CSeq_loc

* GetFirstLoc(ENullSegType null_seg = eNullSegAllow)

const

;

109  const CSeq_loc

* GetLastLoc (ENullSegType null_seg = eNullSegAllow)

const

;

110  CSeq_loc

* SetFirstLoc(ENullSegType null_seg = eNullSegAllow);

111  CSeq_loc

* SetLastLoc (ENullSegType null_seg = eNullSegAllow);

113

ENullSegType null_seg = eNullSegAllow)

const

;

115

ENullSegType null_seg = eNullSegAllow)

const

;

117

ENullSegType null_seg = eNullSegAllow);

119

ENullSegType null_seg = eNullSegAllow);

125  void

ResetStrand(

void

);

128  void

FlipStrand(

void

);

bool IsReverse(ENa_strand s)

ESeqLocExtremes

Used to determine the meaning of a location's Start/Stop positions.

EIsSetStrand

Flag used by IsSetStrand() to switch between any/all modes.

@ eIsSetStrand_Any

Check if any part has strand.

bool IsReverseStrand(void) const

ENa_strand GetStrand(void) const

CSeq_loc_mix(const CSeq_loc_mix &)

CSeq_loc_mix_Base Tparent

unsigned int TSeqPos

Type for sequence locations and lengths.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_SEQLOC_EXPORT

ENa_strand

strand of nucleic acid

CSeq_loc_mix_Base & operator=(const CSeq_loc_mix_Base &)

void AddInterval(TRangeVec &intervals, TSeqPos from, TSeqPos to, bool from_fuzz=false, bool to_fuzz=false)

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