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

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vector< CRange<TSeqPos> >

;

AddIntervals(

& ivals);

IsReverseStrand(

)

;

ResetStrand(

);

FlipStrand(

);

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.

CPacked_seqint(const CPacked_seqint &)

CPacked_seqint_Base Tparent

bool IsReverseStrand(void) const

vector< CRange< TSeqPos > > TRanges

ENa_strand GetStrand(void) const

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.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

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

CPacked_seqint_Base & operator=(const CPacked_seqint_Base &)

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

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

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