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NCBI C++ ToolKit: include/objmgr/bioseq_set_handle.hpp Source File

1 #ifndef OBJMGR__BIOSEQ_SET_HANDLE__HPP 2 #define OBJMGR__BIOSEQ_SET_HANDLE__HPP 145  bool

IsEmptySeq_set(

void

)

const

;

149  bool

IsSetId(

void

)

const

;

150  bool

CanGetId(

void

)

const

;

154  bool

IsSetColl(

void

)

const

;

155  bool

CanGetColl(

void

)

const

;

156  const TColl

& GetColl(

void

)

const

;

159  bool

IsSetLevel(

void

)

const

;

160  bool

CanGetLevel(

void

)

const

;

161  TLevel

GetLevel(

void

)

const

;

164  bool

IsSetClass(

void

)

const

;

165  bool

CanGetClass(

void

)

const

;

166  TClass

GetClass(

void

)

const

;

169  bool

IsSetRelease(

void

)

const

;

170  bool

CanGetRelease(

void

)

const

;

171  const TRelease

& GetRelease(

void

)

const

;

174  bool

IsSetDate(

void

)

const

;

175  bool

CanGetDate(

void

)

const

;

176  const TDate

& GetDate(

void

)

const

;

179  bool

IsSetDescr(

void

)

const

;

180  bool

CanGetDescr(

void

)

const

;

181  const TDescr

& GetDescr(

void

)

const

;

184  bool

HasAnnots(

void

)

const

;

194  bool

IsRemoved(

void

)

const

;

246  typedef int

TComplexityTable[25];

247  static const

TComplexityTable& sx_GetComplexityTable(

void

);

253  const TScopeInfo

& x_GetScopeInfo(

void

)

const

;

278  void

ResetId(

void

)

const

;

279  void

SetId(

TId

&

id

)

const

;

281  void

ResetColl(

void

)

const

;

282  void

SetColl(

TColl

& v)

const

;

284  void

ResetLevel(

void

)

const

;

285  void

SetLevel(

TLevel

v)

const

;

287  void

ResetClass(

void

)

const

;

288  void

SetClass(

TClass

v)

const

;

290  void

ResetRelease(

void

)

const

;

291  void

SetRelease(

TRelease

& v)

const

;

293  void

ResetDate(

void

)

const

;

294  void

SetDate(

TDate

& v)

const

;

296  void

ResetDescr(

void

)

const

;

297  void

SetDescr(

TDescr

& v)

const

;

298  TDescr

& SetDescr(

void

)

const

;

299  bool

AddSeqdesc(

CSeqdesc

& d)

const

;

302  void

AddSeq_descr(

TDescr

& v)

const

;

371  int

index = -1)

const

;

387  int

index = -1)

const

;

403  int

index = -1)

const

;

420  int

index = -1)

const

;

422  int

index = -1)

const

;

439  int

index = -1)

const

;

456  int

index = -1)

const

;

474  int

index = -1)

const

;

481  void

Remove(ERemoveMode

mode

= eRemoveSeq_entry)

const

;

491  void

x_Detach(

void

)

const

;

506  void

x_RealResetId(

void

)

const

;

507  void

x_RealSetId(

TId

&

id

)

const

;

508  void

x_RealResetColl(

void

)

const

;

509  void

x_RealSetColl(

TColl

& v)

const

;

510  void

x_RealResetLevel(

void

)

const

;

511  void

x_RealSetLevel(

TLevel

v)

const

;

512  void

x_RealResetClass(

void

)

const

;

513  void

x_RealSetClass(

TClass

v)

const

;

514  void

x_RealResetRelease(

void

)

const

;

515  void

x_RealSetRelease(

TRelease

& v)

const

;

516  void

x_RealResetDate(

void

)

const

;

517  void

x_RealSetDate(

TDate

& v)

const

;

CBioseq_set_EditHandle –.

const CTSE_Handle & GetTSE_Handle(void) const

const CTSE_Info_Object & GetObjectInfo_Base(void) const

bool IsRemoved(void) const

TScopeInfo & GetNCObject(void) const

@Seq_descr.hpp User-defined methods of the data storage class.

CScope_Impl & x_GetScopeImpl(void) const

CScope & GetScope(void) const

Returns scope.

bool operator<(const CEquivRange &A, const CEquivRange &B)

bool operator==(const CEquivRange &A, const CEquivRange &B)

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

const TScopeInfo & x_GetScopeInfo(void) const

CBioseq_set::TClass TClass

DECLARE_OPERATOR_BOOL(m_Info.IsValid())

Check if handle points to a bioseq-set.

const CTSE_Handle & GetTSE_Handle(void) const

TScopeInfo & x_GetScopeInfo(void) const

void x_RealResetDescr(void) const

CBioseq_set TObject

Unified interface for templates.

CBioseq_set::TLevel TLevel

CConstRef< TObject > GetObjectCore(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

void x_RealSetDescr(TDescr &v) const

CBioseq_set_ScopeInfo(const CTSE_Handle &tse, const TObjectInfo &info)

bool IsRemoved(void) const

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

TObjectInfo & GetNCObjectInfo(void)

CBioseq_set_Info TObjectInfo

bool operator==(const CBioseq_set_Handle &handle) const

Check if handles point to the same bioseq.

CConstRef< TObject > GetCompleteObject(void) const

CBioseq_set_ScopeInfo TScopeInfo

static TComplexityTable sm_ComplexityTable

bool operator<(const CBioseq_set_Handle &handle) const

For usage in containers.

void x_RealAddSeq_descr(TDescr &v) const

CBioseq_set::TRelease TRelease

bool operator!=(const CBioseq_set_Handle &handle) const

CBioseq_set_EditHandle(void)

bool x_RealAddSeqdesc(CSeqdesc &v) const

CScope_Impl & x_GetScopeImpl(void) const

CRef< CSeqdesc > x_RealRemoveSeqdesc(const CSeqdesc &v) const

CRef< CSeqdesc > x_RealReplaceSeqdesc(const CSeqdesc &old_desc, CSeqdesc &new_desc) const

CScopeInfo_Ref< TScopeInfo > TLock

CSeq_entry_Info & x_GetInfo(void) const

CBioseq_set::TDescr TDescr

CConstRef< CBioseq_set > GetBioseq_setCore(void) const

Return core data for the bioseq-set.

friend class CBioseq_set_EditHandle

TScopeInfo & x_GetScopeInfo(void) const

const TObjectInfo & GetObjectInfo(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

#define NCBI_XOBJMGR_EXPORT

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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