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CSeq_entry_EditHandle Class Reference

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CSeq_entry_Handle –. More...

#include <objmgr/seq_entry_handle.hpp>

+ Inheritance diagram for CSeq_entry_EditHandle:
+ Collaboration diagram for CSeq_entry_EditHandle:

Public Types

typedef CBioseq_EditHandle TSeq
 
typedef CBioseq_set_EditHandle TSet
 
- Public Types inherited from CSeq_entry_Handle
typedef CSeq_entry TObject
 Unified interface for templates. More...
 
typedef CSeq_entry::E_Choice E_Choice
 
typedef CBioseq_Handle TSeq
 
typedef CBioseq_set_Handle TSet
 
typedef CSeq_descr TDescr
 
typedef CBioseq_set::TClass TClass
 
typedef CBlobIdKey TBlobId
 
typedef int TBlobVersion
 

Public Member Functions

 CSeq_entry_EditHandle (void)
 
 CSeq_entry_EditHandle (const CSeq_entry_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...
 
CBioseq_set_EditHandle GetParentBioseq_set (void) const
 Get parent bioseq-set edit handle. More...
 
CSeq_entry_EditHandle GetParentEntry (void) const
 Get parent seq-entry edit handle. More...
 
CSubmit_blockSetTopLevelSubmit_block (void) const
 Seq-submit support. More...
 
void SetTopLevelSubmit_block (CSubmit_block &sub) const
 
CSeq_entry_EditHandle GetSingleSubEntry (void) const
 Get edit handle of the sub seq-entry If current seq-entry is not seq-set or has more than one subentry exception is thrown. More...
 
void SetDescr (TDescr &v) const
 
TDescrSetDescr (void) const
 
void ResetDescr (void) const
 
bool AddSeqdesc (CSeqdesc &v) const
 
CRef< CSeqdescRemoveSeqdesc (const CSeqdesc &v) const
 
CRef< CSeqdescReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc) const
 
void AddDescr (TDescr &v) const
 
TSet SetSet (void) const
 
TSeq SetSeq (void) const
 
void SelectNone (void) const
 Make this Seq-entry to be empty. More...
 
TSet SelectSet (TClass set_class=CBioseq_set::eClass_not_set) const
 Convert the empty Seq-entry to Bioseq-set. More...
 
TSet SelectSet (CBioseq_set &seqset) const
 Make the empty Seq-entry be in set state with given Bioseq-set object. More...
 
TSet SelectSet (CRef< CBioseq_set_Info >) const
 
TSet CopySet (const CBioseq_set_Handle &seqset) const
 Make the empty Seq-entry be in set state with given Bioseq-set object. More...
 
TSet TakeSet (const TSet &seqset) const
 Make the empty Seq-entry be in set state with moving Bioseq-set object from the argument seqset. More...
 
TSet SelectSet (const TSet &seqset) const
 Make the empty Seq-entry be in set state with Bioseq-set object from the argument seqset. More...
 
TSeq SelectSeq (CBioseq &seq) const
 Make the empty Seq-entry be in seq state with specified Bioseq object. More...
 
TSeq SelectSeq (CRef< CBioseq_Info > seq) const
 
TSeq CopySeq (const CBioseq_Handle &seq) const
 Make the empty Seq-entry be in seq state with specified Bioseq object. More...
 
TSeq TakeSeq (const TSeq &seq) const
 Make the empty Seq-entry be in seq state with moving bioseq object from the argument seq. More...
 
TSeq SelectSeq (const TSeq &seq) const
 Make the empty Seq-entry be in seq state with Bioseq object from the argument seqset. More...
 
TSet ConvertSeqToSet (TClass set_class=CBioseq_set::eClass_not_set) const
 Convert the entry from Bioseq to Bioseq-set. More...
 
void CollapseSet (void) const
 Collapse one level of Bioseq-set. More...
 
TSeq ConvertSetToSeq (void) const
 Do the same as CollapseSet() when sub-entry is of type bioseq. More...
 
CSeq_annot_EditHandle AttachAnnot (CSeq_annot &annot) const
 Attach an annotation. More...
 
CSeq_annot_EditHandle AttachAnnot (CRef< CSeq_annot_Info > annot) const
 
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...
 
CSeq_annot_EditHandle AttachAnnot (const CSeq_annot_EditHandle &annot) const
 Attach an annotation. More...
 
void TakeAllAnnots (const CSeq_entry_EditHandle &src_entry) const
 Remove all the annotation from seq-entry and attach to current one. More...
 
void TakeAllDescr (const CSeq_entry_EditHandle &src_entry) const
 Remove all the descritions from seq-entry and attach to current one. More...
 
CBioseq_EditHandle AttachBioseq (CBioseq &seq, int index=-1) const
 Attach an existing bioseq. More...
 
CBioseq_EditHandle CopyBioseq (const CBioseq_Handle &seq, int index=-1) const
 Attach a copy of the existing 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 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
 Add removed seq-entry. More...
 
void Remove (void) const
 Remove this Seq-entry from parent, or scope if it's top level Seq-entry. More...
 
void UpdateAnnotations (void) const
 Update annotation index after manual modification of the object. More...
 
TScopeInfox_GetScopeInfo (void) const
 
CSeq_entry_Infox_GetInfo (void) const
 
void x_RealSetDescr (TDescr &v) const
 
void x_RealResetDescr (void) const
 
bool x_RealAddSeqdesc (CSeqdesc &v) const
 
CRef< CSeqdescx_RealRemoveSeqdesc (const CSeqdesc &v) const
 
CRef< CSeqdescx_RealReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc) const
 
void x_RealAddSeq_descr (TDescr &v) const
 
- Public Member Functions inherited from CSeq_entry_Handle
 CSeq_entry_Handle (void)
 
 CSeq_entry_Handle (const CTSE_Handle &tse)
 
CScopeGetScope (void) const
 Get scope this handle belongs to. More...
 
const CBioObjectIdGetBioObjectId (void) const
 Get unique object id. More...
 
bool HasParentEntry (void) const
 Check if current seq-entry has a parent. More...
 
CBioseq_set_Handle GetParentBioseq_set (void) const
 Get parent bioseq-set handle. More...
 
CSeq_entry_Handle GetParentEntry (void) const
 Get parent Seq-entry handle. More...
 
CSeq_entry_Handle GetSingleSubEntry (void) const
 Get handle of the sub seq-entry If current seq-entry is not seq-set or has more than one subentry exception is thrown. More...
 
bool IsTopLevelEntry (void) const
 Check if this handle is top-level entry. More...
 
CSeq_entry_Handle GetTopLevelEntry (void) const
 Get top level Seq-entry handle. More...
 
bool IsTopLevelSeq_submit (void) const
 Seq-submit access functions. More...
 
const CSeq_submitGetTopLevelSeq_submit (void) const
 
const CSubmit_blockGetTopLevelSubmit_block (void) const
 
CBioseq_Handle GetBioseqHandle (const CSeq_id &id) const
 Get Bioseq handle from the TSE of this Seq-entry. More...
 
CBioseq_Handle GetBioseqHandle (const CSeq_id_Handle &id) const
 
CSeq_entry_EditHandle GetEditHandle (void) const
 Get 'edit' version of handle. More...
 
CConstRef< CSeq_entryGetCompleteSeq_entry (void) const
 Complete and get const reference to the seq-entry. More...
 
CConstRef< CSeq_entryGetSeq_entryCore (void) const
 Get const reference to the seq-entry. More...
 
CConstRef< TObjectGetCompleteObject (void) const
 
CConstRef< TObjectGetObjectCore (void) const
 
E_Choice Which (void) const
 
bool IsSeq (void) const
 
TSeq GetSeq (void) const
 
bool IsSet (void) const
 
TSet GetSet (void) const
 
bool IsSetDescr (void) const
 
const TDescrGetDescr (void) const
 
TBlobId GetBlobId (void) const
 
TBlobVersion GetBlobVersion (void) const
 
 DECLARE_OPERATOR_BOOL (m_Info.IsValid())
 
bool IsRemoved (void) const
 
const CTSE_HandleGetTSE_Handle (void) const
 
void Reset (void)
 Reset handle and make it not to point to any seq-entry. More...
 
void Swap (CSeq_entry_Handle &h)
 Reset handle and make it not to point to any seq-entry. More...
 
bool operator== (const CSeq_entry_Handle &handle) const
 Check if handles point to the same seq-entry. More...
 
bool operator!= (const CSeq_entry_Handle &handle) const
 
bool operator< (const CSeq_entry_Handle &handle) const
 For usage in containers. More...
 
const TScopeInfox_GetScopeInfo (void) const
 
const CSeq_entry_Infox_GetInfo (void) const
 

Protected Member Functions

 CSeq_entry_EditHandle (CSeq_entry_Info &info, const CTSE_Handle &tse)
 
- Protected Member Functions inherited from CSeq_entry_Handle
 CSeq_entry_Handle (const CSeq_entry_Info &info, const CTSE_Handle &tse)
 
CScope_Implx_GetScopeImpl (void) const
 

Friends

class CScope_Impl
 
class CBioseq_EditHandle
 
class CBioseq_set_EditHandle
 
class CSeq_annot_EditHandle
 
class CSeq_entry_I
 

Additional Inherited Members

- Protected Types inherited from CSeq_entry_Handle
typedef CSeq_entry_ScopeInfo TScopeInfo
 
typedef CScopeInfo_Ref< TScopeInfoTLock
 
- Protected Attributes inherited from CSeq_entry_Handle
TLock m_Info
 

Detailed Description

CSeq_entry_Handle –.

Proxy to access seq-entry objects

Definition at line 253 of file seq_entry_handle.hpp.


The documentation for this class was generated from the following files:
Modified on Fri May 24 14:53:39 2024 by modify_doxy.py rev. 669887