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

<

Handle>

<

Handle>

<

Handle>

IsPlainFeat(

)

;

IsTableFeat(

)

;

IsSortedTableFeat(

)

;

IsTableSNP(

)

;

GetRange(

)

;

{

GetRange(); }

GetProductTotalRange(

)

;

IsSetId(

)

;

IsSetData(

)

;

IsSetPartial(

)

;

GetPartial(

)

;

IsSetExcept(

)

;

GetExcept(

)

;

IsSetComment(

)

;

& GetComment(

)

;

IsSetProduct(

)

;

& GetLocation(

)

;

IsSetQual(

)

;

IsSetTitle(

)

;

&

(

)

;

IsSetExt(

)

;

IsSetCit(

)

;

& GetCit(

)

;

IsSetExp_ev(

)

;

IsSetXref(

)

;

IsSetDbxref(

)

;

IsSetPseudo(

)

;

GetPseudo(

)

;

IsSetExcept_text(

)

;

& GetExcept_text(

)

;

IsSetIds(

)

;

IsSetExts(

)

;

GetSNPId(

)

;

& GetSNPSeq_id(

)

;

IsSNPMinusStrand(

)

;

GetSNPWeight(

)

;

GetSNPAllelesCount(

)

;

& GetSNPAllele(

index)

;

IsSetSNPComment(

)

;

& GetSNPComment(

)

;

IsSetSNPQualityCode(

)

;

& GetSNPQualityCodeStr(

)

;

GetSNPQualityCodeOs(vector<char>& os)

;

IsSetSNPExtra(

)

;

& GetSNPExtra(

)

;

IsRemoved(

)

;

kNoAnnotObjectInfo = 0x80000000,

kFeatIndexMask = 0x7fffffff

x_HasAnnotObjectInfo()

;

TFeatIndex x_GetFeatIndex()

;

& x_GetPlainSeq_feat(

)

;

& x_GetSNP_InfoAny(

)

;

& x_GetSNP_Info(

)

;

TFeatIndex feat_index);

Remove(

)

;

Replace(

& new_feat)

;

Update(

)

;

AddQualifier(

& qual_name,

& qual_val);

RemoveQualifier(

& qual_name);

AddDbxref(

& db_name,

& db_key);

AddDbxref(

& db_name,

db_key);

AddExceptText(

& exception_text);

RemoveExceptText(

& exception_text);

AddFeatId(

);

AddFeatId(

&

);

AddFeatXref(

);

AddFeatXref(

&

);

RemoveFeatId(

);

RemoveFeatId(

&

);

RemoveFeatXref(

);

RemoveFeatXref(

&

);

ClearFeatIds(

);

ClearFeatXrefs(

);

SetFeatId(

);

SetFeatId(

&

);

x_RealRemove(

)

;

x_RealReplace(

& new_feat)

;

fIncludeTable = 1<<0,

x_Reset(

);

x_Settle(

);

fIncludeTable = 1<<0,

x_Reset(

);

x_Settle(

);

CSeq_feat_EditHandle –.

namespace ncbi::objects::

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

virtual const string & GetNamedQual(const CTempString &qual_name) const =0

Return a named qualifier.

virtual const CProt_ref * GetProtXref(void) const =0

get protein (if present) from Seq-feat.xref list

virtual CConstRef< CDbtag > GetNamedDbxref(const CTempString &db) const =0

Return a specified DB xref.

virtual const CGene_ref * GetGeneXref(void) const =0

get gene (if present) from Seq-feat.xref list

bool operator<(const CEquivRange &A, const CEquivRange &B)

bool operator==(const CEquivRange &A, const CEquivRange &B)

objects::CSeqFeatData::ESubtype GetFeatSubtype(const string &feat_type)

CVect2< NCBI_PROMOTE(int,U) > operator*(int v1, const CVect2< U > &v2)

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,...

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

CRef< CCreatedFeat_Ref > m_CreatedFeat

bool IsSetExcept(void) const

const SSNP_Info & x_GetSNP_Info(void) const

bool GetExcept(void) const

const CFeat_id & GetId(void) const

const CSeq_feat::TXref & GetXref(void) const

const CSeq_feat_EditHandle * operator->(void) const

bool IsSetComment(void) const

TFeatIndex x_GetFeatIndex() const

CSeq_annot_ftable_I & operator++(void)

const CPub_set & GetCit(void) const

friend class CSeq_annot_EditHandle

bool GetPseudo(void) const

const CSeq_annot_EditHandle & GetAnnot(void) const

bool x_HasAnnotObjectInfo() const

bool x_IsExcluded(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

CScope & GetScope(void) const

const CSeq_feat_Handle * operator->(void) const

const CSeq_feat::TExts & GetExts(void) const

bool IsSetDbxref(void) const

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

bool IsSetExp_ev(void) const

CSeq_feat_EditHandle(void)

bool operator==(const CSeq_feat_Handle &feat) const

CSeq_feat::EExp_ev GetExp_ev(void) const

const CSeqFeatData & GetData(void) const

CSeq_annot_ftable_CI & operator++(void)

bool IsSetTitle(void) const

TWeight GetSNPWeight(void) const

bool IsSetXref(void) const

bool IsSetSNPExtra(void) const

bool IsSetExcept_text(void) const

bool IsSetProduct(void) const

CSeq_annot_Handle m_Seq_annot

bool operator<(const CSeq_feat_Handle &feat) const

CConstRef< CSeq_feat > m_CreatedOriginalFeat

CSeq_feat_EditHandle m_Feat

const string & GetComment(void) const

const CUser_object & GetExt(void) const

bool IsSetIds(void) const

const CSeq_feat_EditHandle & operator*(void) const

TSNPId GetSNPId(void) const

const CSeq_annot_Handle & GetAnnot(void) const

const CSeq_feat::TIds & GetIds(void) const

const string & GetExcept_text(void) const

TRange GetLocationTotalRange(void) const

bool operator!=(const CSeq_feat_Handle &feat) const

bool IsTableSNP(void) const

Check if this is SNP table feature.

CSeq_annot_EditHandle m_Annot

const CSeq_annot_Info & x_GetSeq_annot_Info(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeq_annot_Info & x_GetInfo(void) const

const string & GetTitle(void) const

bool IsSetSNPComment(void) const

bool IsSetExts(void) const

CSeq_annot_EditHandle GetAnnot(void) const

CScope & GetScope(void) const

const CSeq_feat::TDbxref & GetDbxref(void) const

bool IsSetQual(void) const

const CSeq_feat_Handle & operator*(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

DECLARE_OPERATOR_BOOL(m_Feat)

bool IsSetPseudo(void) const

const string & GetSNPComment(void) const

SSNP_Info::TWeight TWeight

CSeq_annot_ftable_CI(void)

const CSeq_feat::TQual & GetQual(void) const

CSeq_annot_ftable_I(void)

bool IsSetSNPQualityCode(void) const

bool IsSetExt(void) const

DECLARE_OPERATOR_BOOL(m_Feat)

bool x_IsExcluded(void) const

DECLARE_OPERATOR_BOOL(m_Seq_annot &&!IsRemoved())

bool IsSetCit(void) const

bool IsSNPMinusStrand(void) const

int32_t Int4

4-byte (32-bit) signed integer

#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.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

#define NCBI_XOBJMGR_EXPORT

E_Choice

Choice variants.

bool IsSetTitle(void) const

for user defined label Check if a value has been assigned to Title data member.

bool IsSetComment(void) const

Check if a value has been assigned to Comment data member.

vector< CRef< CDbtag > > TDbxref

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

const TExts & GetExts(void) const

Get the Exts member data.

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

const TIds & GetIds(void) const

Get the Ids member data.

list< CRef< CUser_object > > TExts

const TTitle & GetTitle(void) const

Get the Title member data.

const TCit & GetCit(void) const

Get the Cit member data.

const TQual & GetQual(void) const

Get the Qual member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

E_Choice

Choice variants.

EExp_ev

evidence for existence of feature

const TData & GetData(void) const

Get the Data member data.

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

list< CRef< CFeat_id > > TIds

bool IsSetExp_ev(void) const

Check if a value has been assigned to Exp_ev data member.

bool IsSetIds(void) const

set of Ids; will replace 'id' field Check if a value has been assigned to Ids data member.

bool IsSetId(void) const

Check if a value has been assigned to Id data member.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TComment & GetComment(void) const

Get the Comment member data.

bool IsSetExts(void) const

set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.

bool IsSetCit(void) const

citations for this feature Check if a value has been assigned to Cit data member.

TExcept GetExcept(void) const

Get the Except member data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

const TExt & GetExt(void) const

Get the Ext member data.

TExp_ev GetExp_ev(void) const

Get the Exp_ev member data.

const GenericPointer< typename T::ValueType > T2 value

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

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

string GetProduct(const CProt_ref &prot_ref)

bool MinusStrand(void) const

TCommentIndex m_CommentIndex

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