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CSeq_feat_Handle Class Reference

Search Toolkit Book for CSeq_feat_Handle

CSeq_feat_Handle –. More...

#include <objmgr/seq_feat_handle.hpp>

+ Inheritance diagram for CSeq_feat_Handle:
+ Collaboration diagram for CSeq_feat_Handle:

Public Types

typedef CRange< TSeqPosTRange
typedef SSNP_Info::TSNPId TSNPId
typedef SSNP_Info::TWeight TWeight

Public Member Functions

 CSeq_feat_Handle (void)
 ~CSeq_feat_Handle (void)
void Reset (void)
 DECLARE_OPERATOR_BOOL (m_Seq_annot &&!IsRemoved())
bool operator== (const CSeq_feat_Handle &feat) const
bool operator!= (const CSeq_feat_Handle &feat) const
bool operator< (const CSeq_feat_Handle &feat) const
CScopeGetScope (void) const
 Get scope this handle belongs to. More...
const CSeq_annot_HandleGetAnnot (void) const
 Get handle to seq-annot for this feature. More...
CConstRef< CSeq_featGetPlainSeq_feat (void) const
 Get current seq-feat. More...
CConstRef< CSeq_featGetOriginalSeq_feat (void) const
virtual CConstRef< CSeq_featGetSeq_feat (void) const
bool IsPlainFeat (void) const
 Check if this is plain feature. More...
bool IsTableFeat (void) const
 Check if this is non-SNP table feature. More...
bool IsSortedTableFeat (void) const
 Check if this is a simple feature from sorted Seq-table. More...
bool IsTableSNP (void) const
 Check if this is SNP table feature. More...
virtual TRange GetRange (void) const
 Get range for current seq-feat. More...
virtual CSeq_id_Handle GetLocationId (void) const
TRange GetLocationTotalRange (void) const
virtual CSeq_id_Handle GetProductId (void) const
virtual TRange GetProductTotalRange (void) const
bool IsSetId (void) const
const CFeat_idGetId (void) const
bool IsSetData (void) const
const CSeqFeatDataGetData (void) const
virtual bool IsSetPartial (void) const
virtual bool GetPartial (void) const
bool IsSetExcept (void) const
bool GetExcept (void) const
bool IsSetComment (void) const
const stringGetComment (void) const
bool IsSetProduct (void) const
virtual const CSeq_locGetProduct (void) const
virtual const CSeq_locGetLocation (void) const
bool IsSetQual (void) const
const CSeq_feat::TQualGetQual (void) const
bool IsSetTitle (void) const
const stringGetTitle (void) const
bool IsSetExt (void) const
const CUser_objectGetExt (void) const
bool IsSetCit (void) const
const CPub_setGetCit (void) const
bool IsSetExp_ev (void) const
CSeq_feat::EExp_ev GetExp_ev (void) const
bool IsSetXref (void) const
const CSeq_feat::TXrefGetXref (void) const
bool IsSetDbxref (void) const
const CSeq_feat::TDbxrefGetDbxref (void) const
bool IsSetPseudo (void) const
bool GetPseudo (void) const
bool IsSetExcept_text (void) const
const stringGetExcept_text (void) const
bool IsSetIds (void) const
const CSeq_feat::TIdsGetIds (void) const
bool IsSetExts (void) const
const CSeq_feat::TExtsGetExts (void) const
CSeqFeatData::E_Choice GetFeatType (void) const
CSeqFeatData::ESubtype GetFeatSubtype (void) const
TSNPId GetSNPId (void) const
const CSeq_idGetSNPSeq_id (void) const
CSeq_id::TGi GetSNPGi (void) const
bool IsSNPMinusStrand (void) const
TWeight GetSNPWeight (void) const
size_t GetSNPAllelesCount (void) const
const stringGetSNPAllele (size_t index) const
bool IsSetSNPComment (void) const
const stringGetSNPComment (void) const
bool IsSetSNPQualityCode (void) const
CUser_field::TData::E_Choice GetSNPQualityCodeWhich (void) const
const stringGetSNPQualityCodeStr (void) const
void GetSNPQualityCodeOs (vector< char > &os) const
bool IsSetSNPExtra (void) const
const stringGetSNPExtra (void) const
bool IsRemoved (void) const
 Return true if this feature was removed already. More...
void Remove (void) const
 Remove the feature from Seq-annot. More...
void Replace (const CSeq_feat &new_feat) const
 Replace the feature with new Seq-feat object. More...
const CGene_refGetGeneXref (void) const
 get gene (if present) from Seq-feat.xref list More...
const CProt_refGetProtXref (void) const
 get protein (if present) from Seq-feat.xref list More...
CConstRef< CDbtagGetNamedDbxref (const CTempString &db) const
 Return a specified DB xref. More...
const stringGetNamedQual (const CTempString &qual_name) const
 Return a named qualifier. More...
- Public Member Functions inherited from ISeq_feat
virtual ~ISeq_feat (void)

Protected Types

enum  { kNoAnnotObjectInfo = 0x80000000 , kFeatIndexMask = 0x7fffffff }
typedef Int4 TFeatIndex

Protected Member Functions

bool x_HasAnnotObjectInfo () const
TFeatIndex x_GetFeatIndex () const
const CSeq_annot_Infox_GetSeq_annot_Info (void) const
const CSeq_annot_SNP_Infox_GetSNP_annot_Info (void) const
const CAnnotObject_Infox_GetAnnotObject_InfoAny (void) const
const CAnnotObject_Infox_GetAnnotObject_Info (void) const
const CSeq_featx_GetPlainSeq_feat (void) const
const SSNP_Infox_GetSNP_InfoAny (void) const
const SSNP_Infox_GetSNP_Info (void) const
 CSeq_feat_Handle (const CSeq_annot_Handle &annot, TFeatIndex feat_index)
 CSeq_feat_Handle (const CSeq_annot_Handle &annot, const SSNP_Info &snp_info, CCreatedFeat_Ref &created_ref)
 CSeq_feat_Handle (CScope &scope, CAnnotObject_Info *info)

Private Attributes

CSeq_annot_Handle m_Seq_annot
TFeatIndex m_FeatIndex
CConstRef< CSeq_featm_CreatedOriginalFeat
CRef< CCreatedFeat_Refm_CreatedFeat


class CMappedFeat
class CFeat_CI
class CCreatedFeat_Ref
class CSeq_annot_Info
class CSeq_annot_Handle
class CSeq_annot_ftable_CI
class CSeq_annot_ftable_I
class CTSE_Handle
class CScope_Impl

Detailed Description

CSeq_feat_Handle –.

Proxy to access the seq-feat objects data

Definition at line 75 of file seq_feat_handle.hpp.

The documentation for this class was generated from the following files:
Modified on Wed Apr 24 14:15:12 2024 by rev. 669887