SSNP_Info Struct Reference

Search Toolkit Book for SSNP_Info

#include <objmgr/impl/snp_info.hpp>

Public Types
enum	ESNP_Type {   eSNP_Simple , eSNP_Bad_WrongMemberSet , eSNP_Bad_WrongTextId , eSNP_Complex_CommentTooBig ,   eSNP_Complex_CommentIndexOverflow , eSNP_Complex_LocationIsNotPoint , eSNP_Complex_LocationIsNotGi , eSNP_Complex_LocationGiIsBad ,   eSNP_Complex_LocationStrandIsBad , eSNP_Complex_IdCountTooLarge , eSNP_Complex_IdCountIsNotOne , eSNP_Complex_AlleleTooBig ,   eSNP_Complex_AlleleIndexOverflow , eSNP_Complex_AlleleCountTooLarge , eSNP_Complex_WeightBadValue , eSNP_Complex_WeightCountIsNotOne ,   eSNP_Complex_BadQAdata , eSNP_Complex_NoPlaceForQAdata , eSNP_Complex_QAdataIndexOverflow , eSNP_Type_last }
enum	{ kMax_PositionDelta = kMax_UI1 }
enum	{ kNo_CommentIndex = kMax_UI1 , kMax_CommentIndex = kNo_CommentIndex - 1 }
enum	{ fwWeightQual = 1 << 0 , fwWeightExt = 1 << 1 , fWeightFlagBits = 2 , kMax_Weight = kMax_UI1>>fWeightFlagBits }
enum	{ kNo_ExtraIndex = kMax_UI2 , kMax_ExtraIndex = kNo_ExtraIndex - 1 }
enum	{ kNo_QualityCodesIndex = kMax_UI2 , kMax_QualityCodesIndex = kNo_QualityCodesIndex - 1 }
enum	{ kMax_AllelesCount = 4 }
enum	{ kNo_AlleleIndex = kMax_UI2 , kMax_AlleleIndex = kNo_AlleleIndex - 1 }
enum	FFlags {   fRemoved = 1 << 0 , fPlusStrand = 1 << 1 , fMinusStrand = 1 << 2 , fFuzzLimTr = 1 << 3 ,   fAlleleReplace = 1 << 4 , fQualityCodesStr = 1 << 5 , fQualityCodesOs = 1 << 6 , fQualityCodesMask = fQualityCodesStr | fQualityCodesOs }
typedef CRange< TSeqPos >	TRange
typedef int	TSNPId
typedef Uint1	TPositionDelta
typedef Uint1	TCommentIndex
typedef Uint1	TWeight
typedef Uint2	TExtraIndex
typedef Uint2	TQualityCodesIndex
typedef Uint2	TAlleleIndex
typedef Uint1	TFlags

Public Member Functions
TSeqPos	GetFrom (void) const
TSeqPos	GetTo (void) const
bool	PlusStrand (void) const
bool	MinusStrand (void) const
bool	IsRemoved (void) const
bool	operator< (const SSNP_Info &snp) const
bool	operator< (TSeqPos end_position) const
bool	NoMore (const TRange &range) const
bool	NotThis (const TRange &range) const
ESNP_Type	ParseSeq_feat (const CSeq_feat &feat, CSeq_annot_SNP_Info &annot_info)
CRef< CSeq_feat >	CreateSeq_feat (const CSeq_annot_SNP_Info &annot_info) const
void	UpdateSeq_feat (CRef< CSeq_feat > &seq_feat, const CSeq_annot_SNP_Info &annot_info) const
void	UpdateSeq_feat (CRef< CSeq_feat > &seq_feat, CRef< CSeq_point > &seq_point, CRef< CSeq_interval > &seq_interval, const CSeq_annot_SNP_Info &annot_info) const
CRef< CSeq_feat >	x_CreateSeq_feat (void) const
void	x_UpdateSeq_featData (CSeq_feat &feat, const CSeq_annot_SNP_Info &annot_info) const
void	x_UpdateSeq_feat (CSeq_feat &feat, const CSeq_annot_SNP_Info &annot_info) const
void	x_UpdateSeq_feat (CSeq_feat &feat, CRef< CSeq_point > &seq_point, CRef< CSeq_interval > &seq_interval, const CSeq_annot_SNP_Info &annot_info) const
bool	HasAlleles (void) const
size_t	GetAllelesCount (void) const
TAlleleIndex	GetAlleleStrIndex (size_t index) const
TExtraIndex	GetExtraIndex (void) const
CUser_field::TData::E_Choice	GetQualityCodesWhich (void) const
TQualityCodesIndex	GetQualityCodesStrIndex (void) const
TQualityCodesIndex	GetQualityCodesOsIndex (void) const
bool	HasLabel (const CSeq_annot_SNP_Info &info) const
string	GetLabel (const CSeq_annot_SNP_Info &info) const

Public Attributes
TSeqPos	m_ToPosition
TSNPId	m_SNP_Id
TFlags	m_Flags
TPositionDelta	m_PositionDelta
TCommentIndex	m_CommentIndex
TWeight	m_Weight
TExtraIndex	m_ExtraIndex
TQualityCodesIndex	m_QualityCodesIndex
TAlleleIndex	m_AllelesIndices [kMax_AllelesCount]

Static Public Attributes
static const char *const	s_SNP_Type_Label [eSNP_Type_last]

Detailed Description

Definition at line 53 of file snp_info.hpp.

Member Typedef Documentation

TAlleleIndex

typedef Uint2 SSNP_Info::TAlleleIndex

Definition at line 152 of file snp_info.hpp.

TCommentIndex

typedef Uint1 SSNP_Info::TCommentIndex

Definition at line 127 of file snp_info.hpp.

TExtraIndex

typedef Uint2 SSNP_Info::TExtraIndex

Definition at line 139 of file snp_info.hpp.

TFlags

typedef Uint1 SSNP_Info::TFlags

Definition at line 158 of file snp_info.hpp.

TPositionDelta

typedef Uint1 SSNP_Info::TPositionDelta

Definition at line 123 of file snp_info.hpp.

TQualityCodesIndex

typedef Uint2 SSNP_Info::TQualityCodesIndex

Definition at line 144 of file snp_info.hpp.

TRange

typedef CRange<TSeqPos> SSNP_Info::TRange

Definition at line 56 of file snp_info.hpp.

TSNPId

typedef int SSNP_Info::TSNPId

Definition at line 122 of file snp_info.hpp.

TWeight

typedef Uint1 SSNP_Info::TWeight

Definition at line 132 of file snp_info.hpp.

Member Enumeration Documentation

anonymous enum

anonymous enum

Enumerator
kMax_PositionDelta

Definition at line 124 of file snp_info.hpp.

anonymous enum

anonymous enum

Enumerator
kNo_CommentIndex
kMax_CommentIndex

Definition at line 128 of file snp_info.hpp.

anonymous enum

anonymous enum

Enumerator
fwWeightQual
fwWeightExt
fWeightFlagBits
kMax_Weight

Definition at line 133 of file snp_info.hpp.

anonymous enum

anonymous enum

Enumerator
kNo_ExtraIndex
kMax_ExtraIndex

Definition at line 140 of file snp_info.hpp.

anonymous enum

anonymous enum

Enumerator
kNo_QualityCodesIndex
kMax_QualityCodesIndex

Definition at line 145 of file snp_info.hpp.

anonymous enum

anonymous enum

Enumerator
kMax_AllelesCount

Definition at line 149 of file snp_info.hpp.

anonymous enum

anonymous enum

Enumerator
kNo_AlleleIndex
kMax_AlleleIndex

Definition at line 153 of file snp_info.hpp.

ESNP_Type

enum SSNP_Info::ESNP_Type

Enumerator
eSNP_Simple
eSNP_Bad_WrongMemberSet
eSNP_Bad_WrongTextId
eSNP_Complex_CommentTooBig
eSNP_Complex_CommentIndexOverflow
eSNP_Complex_LocationIsNotPoint
eSNP_Complex_LocationIsNotGi
eSNP_Complex_LocationGiIsBad
eSNP_Complex_LocationStrandIsBad
eSNP_Complex_IdCountTooLarge
eSNP_Complex_IdCountIsNotOne
eSNP_Complex_AlleleTooBig
eSNP_Complex_AlleleIndexOverflow
eSNP_Complex_AlleleCountTooLarge
eSNP_Complex_WeightBadValue
eSNP_Complex_WeightCountIsNotOne
eSNP_Complex_BadQAdata
eSNP_Complex_NoPlaceForQAdata
eSNP_Complex_QAdataIndexOverflow
eSNP_Type_last

Definition at line 72 of file snp_info.hpp.

FFlags

enum SSNP_Info::FFlags

Enumerator
fRemoved
fPlusStrand
fMinusStrand
fFuzzLimTr
fAlleleReplace
fQualityCodesStr
fQualityCodesOs
fQualityCodesMask

Definition at line 159 of file snp_info.hpp.

Member Function Documentation

CreateSeq_feat()

CRef< CSeq_feat > SSNP_Info::CreateSeq_feat

(

const CSeq_annot_SNP_Info &

annot_info

)

const

Definition at line 755 of file snp_annot_info.cpp.

References x_CreateSeq_feat(), and x_UpdateSeq_feat().

GetAllelesCount()

size_t SSNP_Info::GetAllelesCount

(

void

)

const

Definition at line 115 of file snp_annot_info.cpp.

References count, kMax_AllelesCount, kNo_AlleleIndex, and m_AllelesIndices.

Referenced by GetAlleleStrIndex(), and CSeq_feat_Handle::GetSNPAllelesCount().

GetAlleleStrIndex()

SSNP_Info::TAlleleIndex SSNP_Info::GetAlleleStrIndex ( size_t  index ) const

inline

Definition at line 274 of file snp_info.hpp.

References _ASSERT, GetAllelesCount(), and m_AllelesIndices.

GetExtraIndex()

SSNP_Info::TExtraIndex SSNP_Info::GetExtraIndex ( void  ) const

inline

Definition at line 289 of file snp_info.hpp.

References m_ExtraIndex.

GetFrom()

TSeqPos SSNP_Info::GetFrom ( void  ) const

inline

Definition at line 197 of file snp_info.hpp.

References m_PositionDelta, and m_ToPosition.

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), and NotThis().

GetLabel()

string SSNP_Info::GetLabel

(

const CSeq_annot_SNP_Info &

info

)

const

Definition at line 785 of file snp_annot_info.cpp.

References count, kMax_AllelesCount, kNo_AlleleIndex, m_AllelesIndices, str(), and CSeq_annot_SNP_Info::x_GetAllele().

Referenced by CSeq_annot_SNP_Info::GetLabel().

GetQualityCodesOsIndex()

SSNP_Info::TQualityCodesIndex SSNP_Info::GetQualityCodesOsIndex ( void  ) const

inline

Definition at line 304 of file snp_info.hpp.

References _ASSERT, fQualityCodesOs, m_Flags, and m_QualityCodesIndex.

GetQualityCodesStrIndex()

SSNP_Info::TQualityCodesIndex SSNP_Info::GetQualityCodesStrIndex ( void  ) const

inline

Definition at line 296 of file snp_info.hpp.

References _ASSERT, fQualityCodesStr, m_Flags, and m_QualityCodesIndex.

GetQualityCodesWhich()

CUser_field::TData::E_Choice SSNP_Info::GetQualityCodesWhich

(

void

)

const

Definition at line 127 of file snp_annot_info.cpp.

References CUser_field_Base::C_Data::e_not_set, CUser_field_Base::C_Data::e_Os, CUser_field_Base::C_Data::e_Str, fQualityCodesOs, fQualityCodesStr, and m_Flags.

Referenced by CSeq_feat_Handle::GetSNPQualityCodeWhich().

GetTo()

TSeqPos SSNP_Info::GetTo ( void  ) const

inline

Definition at line 204 of file snp_info.hpp.

References m_ToPosition.

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), and NoMore().

HasAlleles()

bool SSNP_Info::HasAlleles ( void  ) const

inline

Definition at line 267 of file snp_info.hpp.

References kNo_AlleleIndex, and m_AllelesIndices.

Referenced by HasLabel().

HasLabel()

bool SSNP_Info::HasLabel ( const CSeq_annot_SNP_Info &  info ) const

inline

Definition at line 282 of file snp_info.hpp.

References HasAlleles().

Referenced by CSeq_annot_SNP_Info::HasLabel().

IsRemoved()

bool SSNP_Info::IsRemoved ( void  ) const

inline

Definition at line 225 of file snp_info.hpp.

References fRemoved, and m_Flags.

Referenced by CSeq_feat_Handle::IsRemoved().

MinusStrand()

bool SSNP_Info::MinusStrand ( void  ) const

inline

Definition at line 218 of file snp_info.hpp.

References fMinusStrand, and m_Flags.

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), CSeq_feat_Handle::IsSNPMinusStrand(), and x_UpdateSeq_feat().

NoMore()

bool SSNP_Info::NoMore ( const TRange &  range ) const

inline

Definition at line 252 of file snp_info.hpp.

References GetTo(), kInvalidSeqPos, kMax_PositionDelta, min(), and compile_time_bits::range().

Referenced by CAnnot_Collector::x_SearchObjects().

NotThis()

bool SSNP_Info::NotThis ( const TRange &  range ) const

inline

Definition at line 260 of file snp_info.hpp.

References GetFrom(), and compile_time_bits::range().

Referenced by CAnnot_Collector::x_SearchObjects().

operator<() [1/2]

bool SSNP_Info::operator< ( const SSNP_Info &  snp ) const

inline

Definition at line 232 of file snp_info.hpp.

References m_ToPosition.

operator<() [2/2]

bool SSNP_Info::operator< ( TSeqPos  end_position ) const

inline

Definition at line 239 of file snp_info.hpp.

References m_ToPosition.

ParseSeq_feat()

SSNP_Info::ESNP_Type SSNP_Info::ParseSeq_feat	(	const CSeq_feat &	feat,
		CSeq_annot_SNP_Info &	annot_info
	)

Definition at line 153 of file snp_annot_info.cpp.

References data, delta(), CObject_id_Base::e_Id, CSeqFeatData_Base::e_Imp, CUser_field_Base::C_Data::e_Int, CSeq_loc_Base::e_Int, CUser_field_Base::C_Data::e_Os, CSeq_loc_Base::e_Pnt, CObject_id_Base::e_Str, CUser_field_Base::C_Data::e_Str, CInt_fuzz_Base::eLim_tr, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, eSNP_Bad_WrongMemberSet, eSNP_Bad_WrongTextId, eSNP_Complex_AlleleCountTooLarge, eSNP_Complex_AlleleIndexOverflow, eSNP_Complex_AlleleTooBig, eSNP_Complex_BadQAdata, eSNP_Complex_CommentIndexOverflow, eSNP_Complex_CommentTooBig, eSNP_Complex_IdCountIsNotOne, eSNP_Complex_IdCountTooLarge, eSNP_Complex_LocationGiIsBad, eSNP_Complex_LocationIsNotPoint, eSNP_Complex_LocationStrandIsBad, eSNP_Complex_NoPlaceForQAdata, eSNP_Complex_QAdataIndexOverflow, eSNP_Complex_WeightBadValue, eSNP_Complex_WeightCountIsNotOne, eSNP_Simple, fAlleleReplace, fFuzzLimTr, fMinusStrand, fPlusStrand, fQualityCodesMask, fQualityCodesOs, fQualityCodesStr, fWeightFlagBits, fwWeightExt, fwWeightQual, CSeq_feat_Base::GetComment(), CUser_field_Base::GetData(), CUser_object_Base::GetData(), CSeq_feat_Base::GetData(), CDbtag_Base::GetDb(), CSeq_feat_Base::GetDbxref(), CSeq_feat_Base::GetExt(), CSeq_interval_Base::GetFrom(), CSeq_point_Base::GetFuzz(), CSeq_interval_Base::GetId(), CSeq_point_Base::GetId(), CUser_field_Base::C_Data::GetInt(), CSeq_loc_Base::GetInt(), CImp_feat_Base::GetKey(), CUser_field_Base::GetLabel(), CInt_fuzz_Base::GetLim(), CSeq_feat_Base::GetLocation(), CUser_field_Base::C_Data::GetOs(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CGb_qual_Base::GetQual(), CSeq_feat_Base::GetQual(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CSeq_interval_Base::GetStrand(), CSeq_loc::GetStrand(), CDbtag_Base::GetTag(), CSeq_interval_Base::GetTo(), CUser_object_Base::GetType(), CGb_qual_Base::GetVal(), i, int, CInt_fuzz_Base::IsLim(), CSeq_feat_Base::IsSetCit(), CSeq_feat_Base::IsSetComment(), CSeq_feat_Base::IsSetDbxref(), CImp_feat_Base::IsSetDescr(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetExp_ev(), CSeq_feat_Base::IsSetExt(), CSeq_point_Base::IsSetFuzz(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_feat_Base::IsSetId(), CImp_feat_Base::IsSetLoc(), CUser_field_Base::IsSetNum(), CSeq_feat_Base::IsSetPartial(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Base::IsSetPseudo(), CSeq_feat_Base::IsSetQual(), CSeq_interval_Base::IsSetStrand(), CSeq_point_Base::IsSetStrand(), CSeq_feat_Base::IsSetTitle(), CSeq_feat_Base::IsSetXref(), CUser_field_Base::C_Data::IsStr(), ITERATE, kId_allele, kId_dbSNP, kId_dbSnpQAdata, kId_dbSnpSynonymyData, kId_Extra, kId_QualityCodes, kId_replace, kId_variation, kId_weight, kMax_AlleleLength, kMax_AllelesCount, kMax_CommentLength, kMax_PositionDelta, kMax_Weight, kNo_AlleleIndex, kNo_CommentIndex, kNo_ExtraIndex, kNo_QualityCodesIndex, kVal_1, m_AllelesIndices, m_CommentIndex, m_ExtraIndex, m_Flags, m_PositionDelta, m_QualityCodesIndex, m_SNP_Id, m_ToPosition, m_Weight, NStr::StringToInt(), tag, rapidjson::value, CObject_id_Base::Which(), CUser_field_Base::C_Data::Which(), CSeq_loc_Base::Which(), CSeq_annot_SNP_Info::x_CheckId(), CSeq_annot_SNP_Info::x_GetAlleleIndex(), CSeq_annot_SNP_Info::x_GetCommentIndex(), CSeq_annot_SNP_Info::x_GetExtraIndex(), and CSeq_annot_SNP_Info::x_GetQualityCodesIndex().

PlusStrand()

bool SSNP_Info::PlusStrand ( void  ) const

inline

Definition at line 211 of file snp_info.hpp.

References fPlusStrand, and m_Flags.

Referenced by CAnnotObject_Ref::CAnnotObject_Ref(), and x_UpdateSeq_feat().

UpdateSeq_feat() [1/2]

void SSNP_Info::UpdateSeq_feat	(	CRef< CSeq_feat > &	seq_feat,
		const CSeq_annot_SNP_Info &	annot_info
	)		const

Definition at line 763 of file snp_annot_info.cpp.

References CObject::ReferencedOnlyOnce(), x_CreateSeq_feat(), and x_UpdateSeq_feat().

Referenced by CCreateFeat::GetOriginalFeat(), and CCreatedFeat_Ref::GetOriginalFeature().

UpdateSeq_feat() [2/2]

void SSNP_Info::UpdateSeq_feat	(	CRef< CSeq_feat > &	seq_feat,
		CRef< CSeq_point > &	seq_point,
		CRef< CSeq_interval > &	seq_interval,
		const CSeq_annot_SNP_Info &	annot_info
	)		const

Definition at line 773 of file snp_annot_info.cpp.

References CObject::ReferencedOnlyOnce(), x_CreateSeq_feat(), and x_UpdateSeq_feat().

x_CreateSeq_feat()

CRef< CSeq_feat > SSNP_Info::x_CreateSeq_feat

(

void

)

const

Definition at line 462 of file snp_annot_info.cpp.

References CPackString::Assign(), data, kId_dbSNP, kId_dbSnpSynonymyData, kId_variation, kId_weight, CSeq_feat_Base::SetData(), CUser_object_Base::SetData(), CDbtag_Base::SetDb(), CSeq_feat_Base::SetDbxref(), CSeq_feat_Base::SetExt(), CUser_field_Base::SetLabel(), and CUser_object_Base::SetType().

Referenced by CreateSeq_feat(), and UpdateSeq_feat().

x_UpdateSeq_feat() [1/2]

void SSNP_Info::x_UpdateSeq_feat	(	CSeq_feat &	feat,
		const CSeq_annot_SNP_Info &	annot_info
	)		const

Definition at line 705 of file snp_annot_info.cpp.

References CInt_fuzz_Base::eLim_tr, eNa_strand_minus, eNa_strand_plus, fFuzzLimTr, CSeq_annot_SNP_Info::GetSeq_id(), m_Flags, m_PositionDelta, m_ToPosition, MinusStrand(), PlusStrand(), CSeq_point_Base::ResetFuzz(), CSeq_interval_Base::ResetStrand(), CSeq_point_Base::ResetStrand(), CSeq_interval_Base::SetFrom(), CSeq_point_Base::SetFuzz(), CSeq_interval_Base::SetId(), CSeq_point_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_point_Base::SetPoint(), CSeq_interval_Base::SetStrand(), CSeq_point_Base::SetStrand(), CSeq_interval_Base::SetTo(), and x_UpdateSeq_featData().

Referenced by CreateSeq_feat(), and UpdateSeq_feat().

x_UpdateSeq_feat() [2/2]

void SSNP_Info::x_UpdateSeq_feat	(	CSeq_feat &	feat,
		CRef< CSeq_point > &	seq_point,
		CRef< CSeq_interval > &	seq_interval,
		const CSeq_annot_SNP_Info &	annot_info
	)		const

Definition at line 650 of file snp_annot_info.cpp.

References CInt_fuzz_Base::eLim_tr, eNa_strand_minus, eNa_strand_plus, fFuzzLimTr, CSeq_annot_SNP_Info::GetSeq_id(), m_Flags, m_PositionDelta, m_ToPosition, MinusStrand(), PlusStrand(), CSeq_point_Base::ResetFuzz(), CSeq_interval_Base::ResetStrand(), CSeq_point_Base::ResetStrand(), CSeq_interval_Base::SetFrom(), CSeq_point_Base::SetFuzz(), CSeq_interval_Base::SetId(), CSeq_point_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_point_Base::SetPoint(), CSeq_interval_Base::SetStrand(), CSeq_point_Base::SetStrand(), CSeq_interval_Base::SetTo(), sx_GetUnreferenced(), and x_UpdateSeq_featData().

x_UpdateSeq_featData()

void SSNP_Info::x_UpdateSeq_featData	(	CSeq_feat &	feat,
		const CSeq_annot_SNP_Info &	annot_info
	)		const

Definition at line 505 of file snp_annot_info.cpp.

References CPackString::Assign(), data, fAlleleReplace, fQualityCodesMask, fQualityCodesStr, fWeightFlagBits, fwWeightExt, fwWeightQual, i, int, NStr::IntToString(), kId_allele, kId_dbSNP, kId_dbSnpQAdata, kId_dbSnpSynonymyData, kId_Extra, kId_QualityCodes, kId_replace, kId_variation, kId_weight, kMax_AllelesCount, kNo_AlleleIndex, kNo_CommentIndex, kNo_ExtraIndex, kVal_1, m_AllelesIndices, m_CommentIndex, m_ExtraIndex, m_Flags, m_QualityCodesIndex, m_SNP_Id, m_Weight, Ref(), CObject::ReferencedOnlyOnce(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::ResetExt(), CSeq_feat_Base::SetComment(), CUser_field_Base::SetData(), CSeq_feat_Base::SetData(), CUser_object_Base::SetData(), CDbtag_Base::SetDb(), CSeq_feat_Base::SetDbxref(), CSeq_feat_Base::SetExt(), CUser_field_Base::SetLabel(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), CDbtag_Base::SetTag(), CUser_object_Base::SetType(), CGb_qual_Base::SetVal(), sx_GetUnreferenced(), weight, CSeq_annot_SNP_Info::x_GetAllele(), CSeq_annot_SNP_Info::x_GetComment(), CSeq_annot_SNP_Info::x_GetExtra(), CSeq_annot_SNP_Info::x_GetQualityCodesOs(), and CSeq_annot_SNP_Info::x_GetQualityCodesStr().

Referenced by x_UpdateSeq_feat().

Member Data Documentation

m_AllelesIndices

TAlleleIndex SSNP_Info::m_AllelesIndices[kMax_AllelesCount]

Definition at line 189 of file snp_info.hpp.

Referenced by GetAllelesCount(), GetAlleleStrIndex(), GetLabel(), HasAlleles(), ParseSeq_feat(), and x_UpdateSeq_featData().

m_CommentIndex

TCommentIndex SSNP_Info::m_CommentIndex

Definition at line 185 of file snp_info.hpp.

Referenced by CSeq_feat_Handle::IsSetSNPComment(), ParseSeq_feat(), and x_UpdateSeq_featData().

m_ExtraIndex

TExtraIndex SSNP_Info::m_ExtraIndex

Definition at line 187 of file snp_info.hpp.

Referenced by GetExtraIndex(), CSeq_feat_Handle::IsSetSNPExtra(), ParseSeq_feat(), and x_UpdateSeq_featData().

m_Flags

TFlags SSNP_Info::m_Flags

Definition at line 183 of file snp_info.hpp.

Referenced by GetQualityCodesOsIndex(), GetQualityCodesStrIndex(), GetQualityCodesWhich(), IsRemoved(), MinusStrand(), ParseSeq_feat(), PlusStrand(), x_UpdateSeq_feat(), and x_UpdateSeq_featData().

m_PositionDelta

TPositionDelta SSNP_Info::m_PositionDelta

Definition at line 184 of file snp_info.hpp.

Referenced by GetFrom(), ParseSeq_feat(), and x_UpdateSeq_feat().

m_QualityCodesIndex

TQualityCodesIndex SSNP_Info::m_QualityCodesIndex

Definition at line 188 of file snp_info.hpp.

Referenced by GetQualityCodesOsIndex(), GetQualityCodesStrIndex(), ParseSeq_feat(), and x_UpdateSeq_featData().

m_SNP_Id

TSNPId SSNP_Info::m_SNP_Id

Definition at line 182 of file snp_info.hpp.

Referenced by CSeq_feat_Handle::GetSNPId(), ParseSeq_feat(), and x_UpdateSeq_featData().

m_ToPosition

TSeqPos SSNP_Info::m_ToPosition

Definition at line 181 of file snp_info.hpp.

Referenced by GetFrom(), GetTo(), operator<(), operator<(), ParseSeq_feat(), and x_UpdateSeq_feat().

m_Weight

TWeight SSNP_Info::m_Weight

Definition at line 186 of file snp_info.hpp.

Referenced by CSeq_feat_Handle::GetSNPWeight(), ParseSeq_feat(), and x_UpdateSeq_featData().

s_SNP_Type_Label

const char *const SSNP_Info::s_SNP_Type_Label

static

Initial value:

= {
    "simple",
    "bad - wrong member set",
    "bad - wrong text id",
    "complex - comment too big",
    "complex - comment index overflow",
    "complex - location is not point",
    "complex - location is not gi",
    "complex - location gi is bad",
    "complex - location strand is bad",
    "complex - id count is too large",
    "complex - id count is not one",
    "complex - allele length is too big",
    "complex - allele index overflow",
    "complex - allele count is too large",
    "complex - weight has bad value",
    "complex - weight count is not one",
    "complex - bad format of dbSnpQAdata",
    "complex - no place for dbSnpQAdata",
    "complex - dbSnpQAdata index overflow"
}

Definition at line 95 of file snp_info.hpp.

---

The documentation for this struct was generated from the following files:

• include/objmgr/impl/snp_info.hpp
• src/objmgr/snp_annot_info.cpp