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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
 

Friends

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 Thu Nov 30 04:55:06 2023 by modify_doxy.py rev. 669887