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

PlusStrand(

)

;

MinusStrand(

)

;

IsRemoved(

)

;

NoMore(

& range)

;

NotThis(

& range)

;

*

s_SNP_Type_Label[eSNP_Type_last];

x_UpdateSeq_featData(

& feat,

kMax_CommentIndex = kNo_CommentIndex - 1

fwWeightQual = 1 << 0,

fwWeightExt = 1 << 1,

kMax_Weight =

>>fWeightFlagBits

kMax_ExtraIndex = kNo_ExtraIndex - 1

kMax_QualityCodesIndex = kNo_QualityCodesIndex - 1

kMax_AllelesCount = 4

kMax_AlleleIndex = kNo_AlleleIndex - 1

fPlusStrand = 1 << 1,

fMinusStrand = 1 << 2,

fAlleleReplace = 1 << 4,

fQualityCodesStr = 1 << 5,

fQualityCodesOs = 1 << 6,

fQualityCodesMask = fQualityCodesStr | fQualityCodesOs

HasAlleles(

)

;

GetAllelesCount(

)

;

TAlleleIndex GetAlleleStrIndex(

index)

;

TExtraIndex GetExtraIndex(

)

;

TQualityCodesIndex GetQualityCodesStrIndex(

)

;

TQualityCodesIndex GetQualityCodesOsIndex(

)

;

namespace ncbi::objects::

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

string GetLabel(const CSeq_id &id)

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

position_type GetToOpen(void) const

#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

E_Choice

Choice variants.

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

bool operator<(TSeqPos end_position, const SSNP_Info &snp)

TExtraIndex GetExtraIndex(void) const

bool IsRemoved(void) const

bool NoMore(const TRange &range) const

TAlleleIndex m_AllelesIndices[kMax_AllelesCount]

TQualityCodesIndex m_QualityCodesIndex

TAlleleIndex GetAlleleStrIndex(size_t index) const

bool NotThis(const TRange &range) const

TSeqPos GetFrom(void) const

TQualityCodesIndex GetQualityCodesStrIndex(void) const

@ eSNP_Complex_LocationGiIsBad

@ eSNP_Complex_LocationIsNotPoint

@ eSNP_Complex_IdCountIsNotOne

@ eSNP_Complex_CommentIndexOverflow

@ eSNP_Bad_WrongMemberSet

@ eSNP_Complex_AlleleCountTooLarge

@ eSNP_Complex_WeightBadValue

@ eSNP_Complex_QAdataIndexOverflow

@ eSNP_Complex_WeightCountIsNotOne

@ eSNP_Complex_LocationStrandIsBad

@ eSNP_Complex_AlleleTooBig

@ eSNP_Complex_NoPlaceForQAdata

@ eSNP_Complex_IdCountTooLarge

@ eSNP_Complex_LocationIsNotGi

@ eSNP_Complex_AlleleIndexOverflow

@ eSNP_Complex_CommentTooBig

bool HasLabel(const CSeq_annot_SNP_Info &info) const

TPositionDelta m_PositionDelta

bool MinusStrand(void) const

bool HasAlleles(void) const

TSeqPos GetTo(void) const

bool operator<(const SSNP_Info &snp) const

size_t GetAllelesCount(void) const

TQualityCodesIndex GetQualityCodesOsIndex(void) const

bool PlusStrand(void) const

TCommentIndex m_CommentIndex

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