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CBioseq_set_EditHandle Class Reference

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CBioseq_set_EditHandle –. More...

#include <objmgr/bioseq_set_handle.hpp>

+ Inheritance diagram for CBioseq_set_EditHandle:
+ Collaboration diagram for CBioseq_set_EditHandle:

Public Types

enum  ERemoveMode { eRemoveSeq_entry , eKeepSeq_entry }
- Public Types inherited from CBioseq_set_Handle
typedef CBioseq_set TObject
 Unified interface for templates. More...
typedef CBioseq_set::TId TId
typedef CBioseq_set::TColl TColl
typedef CBioseq_set::TLevel TLevel
typedef CBioseq_set::TClass TClass
typedef CBioseq_set::TRelease TRelease
typedef CBioseq_set::TDate TDate
typedef CBioseq_set::TDescr TDescr

Public Member Functions

 CBioseq_set_EditHandle (void)
 CBioseq_set_EditHandle (const CBioseq_set_Handle &h)
 create edit interface class to the object which already allows editing throw an exception if the argument is not in editing mode More...
CSeq_entry_EditHandle GetParentEntry (void) const
 Navigate object tree. More...
void ResetId (void) const
void SetId (TId &id) const
void ResetColl (void) const
void SetColl (TColl &v) const
void ResetLevel (void) const
void SetLevel (TLevel v) const
void ResetClass (void) const
void SetClass (TClass v) const
void ResetRelease (void) const
void SetRelease (TRelease &v) const
void ResetDate (void) const
void SetDate (TDate &v) const
void ResetDescr (void) const
void SetDescr (TDescr &v) const
TDescrSetDescr (void) const
bool AddSeqdesc (CSeqdesc &d) const
CRef< CSeqdescRemoveSeqdesc (const CSeqdesc &d) const
CRef< CSeqdescReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc) const
void AddSeq_descr (TDescr &v) const
CSeq_entry_EditHandle AddNewEntry (int index) const
 Create new empty seq-entry. More...
CSeq_annot_EditHandle AttachAnnot (CSeq_annot &annot) const
 Attach an annotation. More...
CSeq_annot_EditHandle CopyAnnot (const CSeq_annot_Handle &annot) const
 Attach a copy of the annotation. More...
CSeq_annot_EditHandle TakeAnnot (const CSeq_annot_EditHandle &annot) const
 Remove the annotation from its location and attach to current one. More...
CBioseq_EditHandle AttachBioseq (CBioseq &seq, int index=-1) const
 Attach a bioseq. More...
CBioseq_EditHandle CopyBioseq (const CBioseq_Handle &seq, int index=-1) const
 Attach a copy of the bioseq. More...
CBioseq_EditHandle TakeBioseq (const CBioseq_EditHandle &seq, int index=-1) const
 Remove bioseq from its location and attach to current one. More...
CSeq_entry_EditHandle AttachEntry (CSeq_entry &entry, int index=-1) const
 Attach an existing seq-entry. More...
CSeq_entry_EditHandle AttachEntry (CRef< CSeq_entry_Info > entry, int index=-1) const
CSeq_entry_EditHandle CopyEntry (const CSeq_entry_Handle &entry, int index=-1) const
 Attach a copy of the existing seq-entry. More...
CSeq_entry_EditHandle TakeEntry (const CSeq_entry_EditHandle &entry, int index=-1) const
 Remove seq-entry from its location and attach to current one. More...
CSeq_entry_EditHandle AttachEntry (const CSeq_entry_EditHandle &entry, int index=-1) const
 Attach seq-entry previously removed from another place. More...
void Remove (ERemoveMode mode=eRemoveSeq_entry) const
 Remove current seqset-entry from its location. More...
TScopeInfox_GetScopeInfo (void) const
CBioseq_set_Infox_GetInfo (void) const
void x_RealResetDescr (void) const
void x_RealSetDescr (TDescr &v) const
bool x_RealAddSeqdesc (CSeqdesc &d) const
CRef< CSeqdescx_RealRemoveSeqdesc (const CSeqdesc &d) const
CRef< CSeqdescx_RealReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc) const
void x_RealAddSeq_descr (TDescr &v) const
void x_RealResetId (void) const
void x_RealSetId (TId &id) const
void x_RealResetColl (void) const
void x_RealSetColl (TColl &v) const
void x_RealResetLevel (void) const
void x_RealSetLevel (TLevel v) const
void x_RealResetClass (void) const
void x_RealSetClass (TClass v) const
void x_RealResetRelease (void) const
void x_RealSetRelease (TRelease &v) const
void x_RealResetDate (void) const
void x_RealSetDate (TDate &v) const
- Public Member Functions inherited from CBioseq_set_Handle
 CBioseq_set_Handle (void)
CScopeGetScope (void) const
 Get scope this handle belongs to. More...
CSeq_entry_Handle GetParentEntry (void) const
 Return a handle for the parent seq-entry of the bioseq. More...
CBioseq_set_Handle GetParentBioseq_set (void) const
 Return a handle for the parent Bioseq-set, or null handle. More...
CSeq_entry_Handle GetTopLevelEntry (void) const
 Return a handle for the top-level seq-entry. More...
CBioseq_set_EditHandle GetEditHandle (void) const
 Get 'edit' version of handle. More...
CConstRef< CBioseq_setGetCompleteBioseq_set (void) const
 Return the complete bioseq-set object. More...
CConstRef< CBioseq_setGetBioseq_setCore (void) const
 Return core data for the bioseq-set. More...
CConstRef< TObjectGetCompleteObject (void) const
CConstRef< TObjectGetObjectCore (void) const
const CBioObjectIdGetBioObjectId (void) const
 Get unique object id. More...
bool IsEmptySeq_set (void) const
 Check if the bioseq set is empty. More...
bool IsSetId (void) const
bool CanGetId (void) const
const TIdGetId (void) const
bool IsSetColl (void) const
bool CanGetColl (void) const
const TCollGetColl (void) const
bool IsSetLevel (void) const
bool CanGetLevel (void) const
TLevel GetLevel (void) const
bool IsSetClass (void) const
bool CanGetClass (void) const
TClass GetClass (void) const
bool IsSetRelease (void) const
bool CanGetRelease (void) const
const TReleaseGetRelease (void) const
bool IsSetDate (void) const
bool CanGetDate (void) const
const TDateGetDate (void) const
bool IsSetDescr (void) const
bool CanGetDescr (void) const
const TDescrGetDescr (void) const
bool HasAnnots (void) const
 Check if handle points to a bioseq-set. More...
bool IsRemoved (void) const
const CTSE_HandleGetTSE_Handle (void) const
void Reset (void)
bool operator== (const CBioseq_set_Handle &handle) const
 Check if handles point to the same bioseq. More...
bool operator!= (const CBioseq_set_Handle &handle) const
bool operator< (const CBioseq_set_Handle &handle) const
 For usage in containers. More...
CSeq_entry_Handle GetComplexityLevel (CBioseq_set::EClass cls) const
 Go up to a certain complexity level (or the nearest level of the same priority if the required class is not found). More...
CSeq_entry_Handle GetExactComplexityLevel (CBioseq_set::EClass cls) const
 Return level with exact complexity, or empty handle if not found. More...
int GetSeq_entry_Index (const CSeq_entry_Handle &handle) const
const TScopeInfox_GetScopeInfo (void) const
const CBioseq_set_Infox_GetInfo (void) const

Protected Member Functions

 CBioseq_set_EditHandle (CBioseq_set_Info &info, const CTSE_Handle &tse)
void x_Detach (void) const
- Protected Member Functions inherited from CBioseq_set_Handle
 CBioseq_set_Handle (const CBioseq_set_Info &info, const CTSE_Handle &tse)
 CBioseq_set_Handle (const TLock &lock)
CScope_Implx_GetScopeImpl (void) const


class CScope_Impl
class CBioseq_EditHandle
class CSeq_entry_EditHandle

Additional Inherited Members

- Protected Types inherited from CBioseq_set_Handle
typedef CBioseq_set_ScopeInfo TScopeInfo
typedef CScopeInfo_Ref< TScopeInfoTLock
typedef int TComplexityTable[25]
- Static Protected Member Functions inherited from CBioseq_set_Handle
static const TComplexityTablesx_GetComplexityTable (void)
- Protected Attributes inherited from CBioseq_set_Handle
TLock m_Info
- Static Protected Attributes inherited from CBioseq_set_Handle
static TComplexityTable sm_ComplexityTable

Detailed Description

CBioseq_set_EditHandle –.

Proxy to access and edit the bioseq_set objects

Definition at line 265 of file bioseq_set_handle.hpp.

The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:00:40 2024 by rev. 669887