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CSeq_feat_EditHandle Class Reference

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CSeq_feat_EditHandle –. More...

#include <objmgr/seq_feat_handle.hpp>

+ Inheritance diagram for CSeq_feat_EditHandle:
+ Collaboration diagram for CSeq_feat_EditHandle:

Public Member Functions

 CSeq_feat_EditHandle (void)
 
 CSeq_feat_EditHandle (const CSeq_feat_Handle &h)
 
CSeq_annot_EditHandle GetAnnot (void) const
 
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...
 
void Update (void) const
 Update index after manual modification of the object. More...
 
void SetGeneXref (CGene_ref &value)
 get gene (if present) from Seq-feat.xref list More...
 
CGene_refSetGeneXref (void)
 
void SetProtXref (CProt_ref &value)
 get protein (if present) from Seq-feat.xref list More...
 
CProt_refSetProtXref (void)
 
void AddQualifier (const string &qual_name, const string &qual_val)
 Add a qualifier to this feature. More...
 
void RemoveQualifier (const string &qual_name)
 Remove all qualifiers with the given name on this feature. More...
 
void AddDbxref (const string &db_name, const string &db_key)
 add a DB xref to this feature More...
 
void AddDbxref (const string &db_name, int db_key)
 
void AddExceptText (const string &exception_text)
 Add the given exception_text and set the except flag to true. More...
 
void RemoveExceptText (const string &exception_text)
 Remove all instances of the given exception text in this feature, and reset the except flag if there are no exception texts left. More...
 
void AddFeatId (int id)
 Add feature id. More...
 
void AddFeatId (const string &id)
 
void AddFeatId (const CObject_id &id)
 
void AddFeatXref (int id)
 
void AddFeatXref (const string &id)
 
void AddFeatXref (const CObject_id &id)
 
void RemoveFeatId (int id)
 Remove feature id. More...
 
void RemoveFeatId (const string &id)
 
void RemoveFeatId (const CObject_id &id)
 
void RemoveFeatXref (int id)
 
void RemoveFeatXref (const string &id)
 
void RemoveFeatXref (const CObject_id &id)
 
void ClearFeatIds (void)
 Clear feature ids. More...
 
void ClearFeatXrefs (void)
 
void SetFeatId (int id)
 Set single feature id. More...
 
void SetFeatId (const string &id)
 
void SetFeatId (const CObject_id &id)
 
- Public Member Functions inherited from CSeq_feat_Handle
 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 Member Functions

 CSeq_feat_EditHandle (const CSeq_annot_EditHandle &annot, TFeatIndex feat_index)
 
 CSeq_feat_EditHandle (const CSeq_annot_EditHandle &annot, const SSNP_Info &snp_info, CCreatedFeat_Ref &created_ref)
 
void x_RealRemove (void) const
 Remove the feature from Seq-annot. More...
 
void x_RealReplace (const CSeq_feat &new_feat) const
 Replace the feature with new Seq-feat object. More...
 
- Protected Member Functions inherited from CSeq_feat_Handle
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)
 

Friends

class CSeq_annot_EditHandle
 
class CSeq_annot_Add_EditCommand< CSeq_feat_EditHandle >
 
class CSeq_annot_Replace_EditCommand< CSeq_feat_EditHandle >
 
class CSeq_annot_Remove_EditCommand< CSeq_feat_EditHandle >
 
class CSeq_annot_ftable_I
 

Additional Inherited Members

- Public Types inherited from CSeq_feat_Handle
typedef CRange< TSeqPosTRange
 
typedef SSNP_Info::TSNPId TSNPId
 
typedef SSNP_Info::TWeight TWeight
 
- Protected Types inherited from CSeq_feat_Handle
enum  { kNoAnnotObjectInfo = 0x80000000 , kFeatIndexMask = 0x7fffffff }
 
typedef Int4 TFeatIndex
 

Detailed Description

CSeq_feat_EditHandle –.

Proxy to edit the seq-feat objects data

Definition at line 606 of file seq_feat_handle.hpp.


The documentation for this class was generated from the following files:
Modified on Sun Jun 23 05:17:19 2024 by modify_doxy.py rev. 669887