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CBioseq_Info Class Reference

Search Toolkit Book for CBioseq_Info

#include <objmgr/impl/bioseq_info.hpp>

+ Inheritance diagram for CBioseq_Info:
+ Collaboration diagram for CBioseq_Info:

Public Types

typedef CBioseq TObject
 
typedef vector< CSeq_id_Handle > TId
 
typedef TObject::TInst TInst
 
typedef TInst::TRepr TInst_Repr
 
typedef TInst::TMol TInst_Mol
 
typedef TInst::TLength TInst_Length
 
typedef TInst::TFuzz TInst_Fuzz
 
typedef TInst::TTopology TInst_Topology
 
typedef TInst::TStrand TInst_Strand
 
typedef TInst::TSeq_data TInst_Seq_data
 
typedef TInst::TExt TInst_Ext
 
typedef TInst::THist TInst_Hist
 
typedef TInst::THist::TAssembly TInst_Hist_Assembly
 
typedef TInst::THist::TReplaces TInst_Hist_Replaces
 
typedef TInst::THist::TReplaced_by TInst_Hist_Replaced_by
 
typedef TInst::THist::TDeleted TInst_Hist_Deleted
 
- Public Types inherited from CBioseq_Base_Info
typedef CSeq_descr TDescr
 
typedef TDescr::Tdata TDescList
 
typedef TDescList::const_iterator TDesc_CI
 
typedef unsigned TDescTypeMask
 
typedef vector< CRef< CSeq_annot_Info > > TAnnot
 
typedef list< CRef< CSeq_annot > > TObjAnnot
 
- Public Types inherited from CTSE_Info_Object
enum  ENeedUpdateAux { kNeedUpdate_bits = 8 }
 
enum  ENeedUpdate {
  fNeedUpdate_this = (1<<kNeedUpdate_bits)-1 , fNeedUpdate_children = fNeedUpdate_this<<kNeedUpdate_bits , fNeedUpdate_descr = 1<<0 , fNeedUpdate_annot = 1<<1 ,
  fNeedUpdate_seq_data = 1<<2 , fNeedUpdate_core = 1<<3 , fNeedUpdate_assembly = 1<<4 , fNeedUpdate_bioseq = 1<<5 ,
  fNeedUpdate_children_descr = fNeedUpdate_descr <<kNeedUpdate_bits , fNeedUpdate_children_annot = fNeedUpdate_annot <<kNeedUpdate_bits , fNeedUpdate_children_seq_data = fNeedUpdate_seq_data<<kNeedUpdate_bits , fNeedUpdate_children_core = fNeedUpdate_core <<kNeedUpdate_bits ,
  fNeedUpdate_children_assembly = fNeedUpdate_assembly<<kNeedUpdate_bits , fNeedUpdate_children_bioseq = fNeedUpdate_bioseq <<kNeedUpdate_bits
}
 
typedef map< CConstRef< CObject >, CRef< CObject > > TObjectCopyMap
 
typedef int TNeedUpdateFlags
 
typedef int TChunkId
 
typedef vector< TChunkId > TChunkIds
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8 > TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CBioseq_Info (const CBioseq_Info &src, TObjectCopyMap *copy_map)
 
 CBioseq_Info (CBioseq &seq)
 
virtual ~CBioseq_Info (void)
 
CConstRef< TObject > GetBioseqCore (void) const
 
CConstRef< TObject > GetCompleteBioseq (void) const
 
bool IsSetId (void) const
 
bool CanGetId (void) const
 
const TId & GetId (void) const
 
void ResetId (void)
 
bool HasId (const CSeq_id_Handle &id) const
 
bool AddId (const CSeq_id_Handle &id)
 
bool RemoveId (const CSeq_id_Handle &id)
 
string IdString (void) const
 
bool x_IsSetDescr (void) const
 
bool x_CanGetDescr (void) const
 
const TDescr & x_GetDescr (void) const
 
TDescr & x_SetDescr (void)
 
void x_SetDescr (TDescr &v)
 
void x_ResetDescr (void)
 
bool IsSetInst (void) const
 
bool CanGetInst (void) const
 
const TInst & GetInst (void) const
 
void SetInst (TInst &v)
 
void ResetInst ()
 
bool IsSetInst_Repr (void) const
 
bool CanGetInst_Repr (void) const
 
TInst_Repr GetInst_Repr (void) const
 
void SetInst_Repr (TInst_Repr v)
 
void ResetInst_Repr ()
 
bool IsSetInst_Mol (void) const
 
bool CanGetInst_Mol (void) const
 
TInst_Mol GetInst_Mol (void) const
 
void SetInst_Mol (TInst_Mol v)
 
void ResetInst_Mol ()
 
bool IsSetInst_Length (void) const
 
bool CanGetInst_Length (void) const
 
TInst_Length GetInst_Length (void) const
 
void SetInst_Length (TInst_Length v)
 
TSeqPos GetBioseqLength (void) const
 
void ResetInst_Length ()
 
bool IsSetInst_Fuzz (void) const
 
bool CanGetInst_Fuzz (void) const
 
const TInst_Fuzz & GetInst_Fuzz (void) const
 
void SetInst_Fuzz (TInst_Fuzz &v)
 
void ResetInst_Fuzz ()
 
bool IsSetInst_Topology (void) const
 
bool CanGetInst_Topology (void) const
 
TInst_Topology GetInst_Topology (void) const
 
void SetInst_Topology (TInst_Topology v)
 
void ResetInst_Topology ()
 
bool IsSetInst_Strand (void) const
 
bool CanGetInst_Strand (void) const
 
TInst_Strand GetInst_Strand (void) const
 
void SetInst_Strand (TInst_Strand v)
 
void ResetInst_Strand ()
 
bool IsSetInst_Seq_data (void) const
 
bool CanGetInst_Seq_data (void) const
 
const TInst_Seq_data & GetInst_Seq_data (void) const
 
void SetInst_Seq_data (TInst_Seq_data &v)
 
void ResetInst_Seq_data ()
 
bool IsSetInst_Ext (void) const
 
bool CanGetInst_Ext (void) const
 
const TInst_Ext & GetInst_Ext (void) const
 
void SetInst_Ext (TInst_Ext &v)
 
void ResetInst_Ext ()
 
bool IsSetInst_Hist (void) const
 
bool CanGetInst_Hist (void) const
 
const TInst_Hist & GetInst_Hist (void) const
 
void SetInst_Hist (TInst_Hist &v)
 
void ResetInst_Hist ()
 
bool IsSetInst_Hist_Assembly (void) const
 
bool CanGetInst_Hist_Assembly (void) const
 
const TInst_Hist_Assembly & GetInst_Hist_Assembly (void) const
 
void SetInst_Hist_Assembly (const TInst_Hist_Assembly &v)
 
bool IsSetInst_Hist_Replaces (void) const
 
bool CanGetInst_Hist_Replaces (void) const
 
const TInst_Hist_Replaces & GetInst_Hist_Replaces (void) const
 
void SetInst_Hist_Replaces (TInst_Hist_Replaces &v)
 
bool IsSetInst_Hist_Replaced_by (void) const
 
bool CanGetInst_Hist_Replaced_by (void) const
 
const TInst_Hist_Replaced_by & GetInst_Hist_Replaced_by (void) const
 
void SetInst_Hist_Replaced_by (TInst_Hist_Replaced_by &v)
 
bool IsSetInst_Hist_Deleted (void) const
 
bool CanGetInst_Hist_Deleted (void) const
 
const TInst_Hist_Deleted & GetInst_Hist_Deleted (void) const
 
void SetInst_Hist_Deleted (TInst_Hist_Deleted &v)
 
bool IsNa (void) const
 
bool IsAa (void) const
 
int GetFeatureFetchPolicy (void) const
 
const CSeqMap & GetSeqMap (void) const
 
TTaxId GetTaxId (void) const
 
int GetSequenceClass (void) const
 
void x_AttachMap (CSeqMap &seq_map)
 
void x_AddSeq_dataChunkId (TChunkId chunk_id)
 
void x_AddAssemblyChunkId (TChunkId chunk_id)
 
void x_DoUpdate (TNeedUpdateFlags flags)
 
- Public Member Functions inherited from CBioseq_Base_Info
 CBioseq_Base_Info (void)
 
 CBioseq_Base_Info (const CBioseq_Base_Info &src, TObjectCopyMap *copy_map)
 
virtual ~CBioseq_Base_Info (void)
 
const CSeq_entry_Info & GetParentSeq_entry_Info (void) const
 
CSeq_entry_Info & GetParentSeq_entry_Info (void)
 
bool IsSetDescr (void) const
 
bool CanGetDescr (void) const
 
const TDescr & GetDescr (void) const
 
TDescr & SetDescr (void)
 
void SetDescr (TDescr &v)
 
void ResetDescr (void)
 
bool AddSeqdesc (CSeqdesc &d)
 
CRef< CSeqdesc > RemoveSeqdesc (const CSeqdesc &d)
 
CRef< CSeqdesc > ReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc)
 
void AddSeq_descr (const TDescr &v)
 
const TDescList & x_GetDescList (void) const
 
TDesc_CI x_GetFirstDesc (TDescTypeMask types) const
 
TDesc_CI x_GetNextDesc (TDesc_CI iter, TDescTypeMask types) const
 
bool x_IsEndDesc (TDesc_CI iter) const
 
const CSeqdesc * x_SearchFirstDesc (TDescTypeMask type) const
 
TDescTypeMask x_GetExistingDescrMask (void) const
 
void x_AddExistingUserObjectTypes (TUserObjectTypesSet &uo_types) const
 
bool IsSetAnnot (void) const
 
bool HasAnnots (void) const
 
const TAnnot & GetAnnot (void) const
 
const TAnnot & GetLoadedAnnot (void) const
 
void ResetAnnot (void)
 
CRef< CSeq_annot_Info > AddAnnot (CSeq_annot &annot, int chunk_id=0)
 
void AddAnnot (CRef< CSeq_annot_Info > annot)
 
void RemoveAnnot (CRef< CSeq_annot_Info > annot)
 
void x_AttachAnnot (CRef< CSeq_annot_Info > info)
 
void x_DetachAnnot (CRef< CSeq_annot_Info > info)
 
void x_UpdateAnnotIndexContents (CTSE_Info &tse)
 
void x_SetAnnot (void)
 
void x_SetAnnot (const CBioseq_Base_Info &info, TObjectCopyMap *copy_map)
 
void x_AddDescrChunkId (const TDescTypeMask &types, TChunkId chunk_id)
 
void x_AddAnnotChunkId (TChunkId chunk_id)
 
const TChunkIds & x_GetDescrChunkIds () const
 
void x_SetNeedUpdateParent (TNeedUpdateFlags flags)
 
void x_RealLoadDescr (const TDescr &v)
 
- Public Member Functions inherited from CTSE_Info_Object
 CTSE_Info_Object (void)
 
 CTSE_Info_Object (const CTSE_Info_Object &src, TObjectCopyMap *copy_map)
 
virtual ~CTSE_Info_Object (void)
 
virtual const CBioObjectId & GetBioObjectId (void) const
 
virtual void SetBioObjectId (const CBioObjectId &id)
 
bool HasDataSource (void) const
 
CDataSource & GetDataSource (void) const
 
bool HasTSE_Info (void) const
 
bool BelongsToTSE_Info (const CTSE_Info &tse) const
 
const CTSE_Info & GetTSE_Info (void) const
 
CTSE_Info & GetTSE_Info (void)
 
bool HasParent_Info (void) const
 
const CTSE_Info_Object & GetBaseParent_Info (void) const
 
CTSE_Info_Object & GetBaseParent_Info (void)
 
void x_DSAttach (CDataSource &ds)
 
void x_DSDetach (CDataSource &ds)
 
void x_TSEAttach (CTSE_Info &tse)
 
void x_TSEDetach (CTSE_Info &tse)
 
bool x_DirtyAnnotIndex (void) const
 
void x_SetDirtyAnnotIndex (void)
 
void x_SetParentDirtyAnnotIndex (void)
 
void x_ResetDirtyAnnotIndex (void)
 
virtual void x_SetDirtyAnnotIndexNoParent (void)
 
virtual void x_ResetDirtyAnnotIndexNoParent (void)
 
void x_UpdateAnnotIndex (CTSE_Info &tse)
 
bool x_NeedUpdate (ENeedUpdate flag) const
 
void x_SetNeedUpdate (TNeedUpdateFlags flags)
 
void x_Update (TNeedUpdateFlags flags) const
 
void x_UpdateComplete (void) const
 
void x_UpdateCore (void) const
 
void x_LoadChunk (TChunkId chunk_id) const
 
void x_LoadChunks (const TChunkIds &chunk_ids) const
 
virtual string GetDescription (void) const
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObject & operator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Protected Member Functions

TObjAnnot & x_SetObjAnnot (void)
 
void x_ResetObjAnnot (void)
 
void x_ResetSeqMap (void)
 
void x_SetChangedSeqMap (void)
 
- Protected Member Functions inherited from CBioseq_Base_Info
bool x_IsEndNextDesc (TDesc_CI iter) const
 
TDesc_CI x_FindDesc (TDescrMutexGuard &guard, TDesc_CI iter, TDescTypeMask types) const
 
void x_PrefetchDesc (TDescrMutexGuard &guard, TDesc_CI last, TDescTypeMask types) const
 
- Protected Member Functions inherited from CTSE_Info_Object
void x_BaseParentAttach (CTSE_Info_Object &parent)
 
void x_BaseParentDetach (CTSE_Info_Object &parent)
 
void x_AttachObject (CTSE_Info_Object &object)
 
void x_DetachObject (CTSE_Info_Object &object)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Types

typedef CBioseq_Base_Info TParent
 

Private Member Functions

CBioseq_Info & operator= (const CBioseq_Info &)
 
void x_DSAttachContents (CDataSource &ds)
 
void x_DSDetachContents (CDataSource &ds)
 
void x_TSEAttachContents (CTSE_Info &tse)
 
void x_TSEDetachContents (CTSE_Info &tse)
 
void x_ParentAttach (CSeq_entry_Info &parent)
 
void x_ParentDetach (CSeq_entry_Info &parent)
 
TObject & x_GetObject (void)
 
const TObject & x_GetObject (void) const
 
void x_SetObject (TObject &obj)
 
void x_SetObject (const CBioseq_Info &info, TObjectCopyMap *copy_map)
 
void x_DSMapObject (CConstRef< TObject > obj, CDataSource &ds)
 
void x_DSUnmapObject (CConstRef< TObject > obj, CDataSource &ds)
 
TSeqPos x_CalcBioseqLength (void) const
 
TSeqPos x_CalcBioseqLength (const CSeq_inst &inst) const
 
TSeqPos x_CalcBioseqLength (const CSeq_id &whole) const
 
TSeqPos x_CalcBioseqLength (const CPacked_seqint &ints) const
 
TSeqPos x_CalcBioseqLength (const CSeq_loc &seq_loc) const
 
TSeqPos x_CalcBioseqLength (const CSeq_loc_mix &seq_mix) const
 
TSeqPos x_CalcBioseqLength (const CSeq_loc_equiv &seq_equiv) const
 
TSeqPos x_CalcBioseqLength (const CSeg_ext &seg_ext) const
 
TSeqPos x_CalcBioseqLength (const CDelta_ext &delta) const
 
TSeqPos x_CalcBioseqLength (const CDelta_seq &delta_seq) const
 

Static Private Member Functions

static CRef< TObject > sx_ShallowCopy (const TObject &obj)
 
static CRef< TInst > sx_ShallowCopy (const TInst &inst)
 

Private Attributes

CRef< TObject > m_Object
 
TId m_Id
 
CRef< CSeqMap > m_SeqMap
 
CFastMutex m_SeqMap_Mtx
 
TChunkIds m_Seq_dataChunks
 
TChunkId m_AssemblyChunk
 
int m_FeatureFetchPolicy
 
atomic< int > m_IdChangeCounter
 

Friends

class CDataSource
 
class CScope_Impl
 
class CTSE_Info
 
class CSeq_entry_Info
 
class CBioseq_set_Info
 
class CSeqMap
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Types inherited from CBioseq_Base_Info
typedef CFastMutex TDescrMutex
 
typedef CFastMutexGuard TDescrMutexGuard
 
typedef vector< TDescTypeMask > TDescTypeMasks
 
- Protected Attributes inherited from CBioseq_Base_Info
TAnnot m_Annot
 
TObjAnnot * m_ObjAnnot
 
TChunkIds m_DescrChunks
 
TDescTypeMasks m_DescrTypeMasks
 
TChunkIds m_AnnotChunks
 
TDescrMutex m_DescrMutex
 

Detailed Description

Definition at line 75 of file bioseq_info.hpp.

Member Typedef Documentation

◆ TId

typedef vector<CSeq_id_Handle> CBioseq_Info::TId

Definition at line 91 of file bioseq_info.hpp.

◆ TInst

typedef TObject::TInst CBioseq_Info::TInst

Definition at line 109 of file bioseq_info.hpp.

◆ TInst_Ext

typedef TInst::TExt CBioseq_Info::TInst_Ext

Definition at line 174 of file bioseq_info.hpp.

◆ TInst_Fuzz

typedef TInst::TFuzz CBioseq_Info::TInst_Fuzz

Definition at line 142 of file bioseq_info.hpp.

◆ TInst_Hist

typedef TInst::THist CBioseq_Info::TInst_Hist

Definition at line 182 of file bioseq_info.hpp.

◆ TInst_Hist_Assembly

typedef TInst::THist::TAssembly CBioseq_Info::TInst_Hist_Assembly

Definition at line 190 of file bioseq_info.hpp.

◆ TInst_Hist_Deleted

typedef TInst::THist::TDeleted CBioseq_Info::TInst_Hist_Deleted

Definition at line 211 of file bioseq_info.hpp.

◆ TInst_Hist_Replaced_by

typedef TInst::THist::TReplaced_by CBioseq_Info::TInst_Hist_Replaced_by

Definition at line 204 of file bioseq_info.hpp.

◆ TInst_Hist_Replaces

typedef TInst::THist::TReplaces CBioseq_Info::TInst_Hist_Replaces

Definition at line 197 of file bioseq_info.hpp.

◆ TInst_Length

typedef TInst::TLength CBioseq_Info::TInst_Length

Definition at line 133 of file bioseq_info.hpp.

◆ TInst_Mol

typedef TInst::TMol CBioseq_Info::TInst_Mol

Definition at line 125 of file bioseq_info.hpp.

◆ TInst_Repr

typedef TInst::TRepr CBioseq_Info::TInst_Repr

Definition at line 117 of file bioseq_info.hpp.

◆ TInst_Seq_data

typedef TInst::TSeq_data CBioseq_Info::TInst_Seq_data

Definition at line 166 of file bioseq_info.hpp.

◆ TInst_Strand

typedef TInst::TStrand CBioseq_Info::TInst_Strand

Definition at line 158 of file bioseq_info.hpp.

◆ TInst_Topology

typedef TInst::TTopology CBioseq_Info::TInst_Topology

Definition at line 150 of file bioseq_info.hpp.

◆ TObject

typedef CBioseq CBioseq_Info::TObject

Definition at line 84 of file bioseq_info.hpp.

◆ TParent

typedef CBioseq_Base_Info CBioseq_Info::TParent
private

Definition at line 77 of file bioseq_info.hpp.

Constructor & Destructor Documentation

◆ CBioseq_Info() [1/2]

CBioseq_Info::CBioseq_Info ( const CBioseq_Info &  src,
TObjectCopyMap *  copy_map 
)
explicit

Definition at line 95 of file bioseq_info.cpp.

References info, CBioseq_Base_Info::m_AnnotChunks, m_AssemblyChunk, CBioseq_Base_Info::m_DescrChunks, m_Seq_dataChunks, and x_SetObject().

◆ CBioseq_Info() [2/2]

CBioseq_Info::CBioseq_Info ( CBioseq &  seq)
explicit

Definition at line 86 of file bioseq_info.cpp.

◆ ~CBioseq_Info()

CBioseq_Info::~CBioseq_Info ( void  )
virtual

Definition at line 113 of file bioseq_info.cpp.

References x_ResetSeqMap().

Member Function Documentation

◆ AddId()

bool CBioseq_Info::AddId ( const CSeq_id_Handle &  id)

Definition at line 431 of file bioseq_info.cpp.

References CSeq_id::Assign(), GetSeqId(), CTSE_Info_Object::GetTSE_Info(), m_Id, m_IdChangeCounter, m_Object, and CTSE_Info::x_SetBioseqId().

Referenced by x_ApplyCmd().

◆ CanGetId()

bool CBioseq_Info::CanGetId ( void  ) const

Definition at line 401 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::CanGetId().

◆ CanGetInst()

bool CBioseq_Info::CanGetInst ( void  ) const

Definition at line 535 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::CanGetInst(), CanGetInst_Fuzz(), CanGetInst_Hist(), CanGetInst_Length(), CanGetInst_Mol(), CanGetInst_Repr(), CanGetInst_Strand(), and CanGetInst_Topology().

◆ CanGetInst_Ext()

bool CBioseq_Info::CanGetInst_Ext ( void  ) const

Definition at line 875 of file bioseq_info.cpp.

References IsSetInst_Ext().

Referenced by CBioseq_Handle::CanGetInst_Ext().

◆ CanGetInst_Fuzz()

bool CBioseq_Info::CanGetInst_Fuzz ( void  ) const

Definition at line 725 of file bioseq_info.cpp.

References CanGetInst(), and m_Object.

Referenced by CBioseq_Handle::CanGetInst_Fuzz().

◆ CanGetInst_Hist()

bool CBioseq_Info::CanGetInst_Hist ( void  ) const

Definition at line 917 of file bioseq_info.cpp.

References CanGetInst(), and m_Object.

Referenced by CBioseq_Handle::CanGetInst_Hist(), CanGetInst_Hist_Assembly(), CanGetInst_Hist_Deleted(), CanGetInst_Hist_Replaced_by(), and CanGetInst_Hist_Replaces().

◆ CanGetInst_Hist_Assembly()

bool CBioseq_Info::CanGetInst_Hist_Assembly ( void  ) const

Definition at line 959 of file bioseq_info.cpp.

References CanGetInst_Hist().

◆ CanGetInst_Hist_Deleted()

bool CBioseq_Info::CanGetInst_Hist_Deleted ( void  ) const

Definition at line 1051 of file bioseq_info.cpp.

References CanGetInst_Hist(), and m_Object.

◆ CanGetInst_Hist_Replaced_by()

bool CBioseq_Info::CanGetInst_Hist_Replaced_by ( void  ) const

Definition at line 1021 of file bioseq_info.cpp.

References CanGetInst_Hist(), and m_Object.

◆ CanGetInst_Hist_Replaces()

bool CBioseq_Info::CanGetInst_Hist_Replaces ( void  ) const

Definition at line 991 of file bioseq_info.cpp.

References CanGetInst_Hist(), and m_Object.

◆ CanGetInst_Length()

bool CBioseq_Info::CanGetInst_Length ( void  ) const

Definition at line 670 of file bioseq_info.cpp.

References CanGetInst(), and m_Object.

Referenced by CBioseq_Handle::CanGetInst_Length().

◆ CanGetInst_Mol()

bool CBioseq_Info::CanGetInst_Mol ( void  ) const

Definition at line 627 of file bioseq_info.cpp.

References CanGetInst(), and m_Object.

Referenced by CBioseq_Handle::CanGetInst_Mol().

◆ CanGetInst_Repr()

bool CBioseq_Info::CanGetInst_Repr ( void  ) const

Definition at line 585 of file bioseq_info.cpp.

References CanGetInst(), and m_Object.

Referenced by CBioseq_Handle::CanGetInst_Repr().

◆ CanGetInst_Seq_data()

bool CBioseq_Info::CanGetInst_Seq_data ( void  ) const

Definition at line 833 of file bioseq_info.cpp.

References IsSetInst_Seq_data().

Referenced by CBioseq_Handle::CanGetInst_Seq_data().

◆ CanGetInst_Strand()

bool CBioseq_Info::CanGetInst_Strand ( void  ) const

Definition at line 793 of file bioseq_info.cpp.

References CanGetInst(), and m_Object.

Referenced by CBioseq_Handle::CanGetInst_Strand().

◆ CanGetInst_Topology()

bool CBioseq_Info::CanGetInst_Topology ( void  ) const

Definition at line 759 of file bioseq_info.cpp.

References CanGetInst(), and m_Object.

Referenced by CBioseq_Handle::CanGetInst_Topology().

◆ GetBioseqCore()

CConstRef< CBioseq > CBioseq_Info::GetBioseqCore ( void  ) const

Definition at line 126 of file bioseq_info.cpp.

References m_Object, and CTSE_Info_Object::x_UpdateCore().

Referenced by CScope_Impl::AddSharedBioseq(), and CBioseq_Handle::GetBioseqCore().

◆ GetBioseqLength()

CBioseq_Info::TInst_Length CBioseq_Info::GetBioseqLength ( void  ) const

Definition at line 704 of file bioseq_info.cpp.

References GetInst_Length(), IsSetInst_Length(), and x_CalcBioseqLength().

Referenced by CDataLoader::GetSequenceLength(), x_CalcBioseqLength(), and CSeqMap::x_ResolveSegmentLength().

◆ GetCompleteBioseq()

CConstRef< CBioseq > CBioseq_Info::GetCompleteBioseq ( void  ) const

Definition at line 119 of file bioseq_info.cpp.

References m_Object, and CTSE_Info_Object::x_UpdateComplete().

Referenced by CBioseq_Handle::GetCompleteBioseq().

◆ GetFeatureFetchPolicy()

int CBioseq_Info::GetFeatureFetchPolicy ( void  ) const

Definition at line 243 of file bioseq_info.cpp.

References CSeqdesc_Base::e_User, CBioseq_Handle::eFeatureFetchPolicy_allow_far, CBioseq_Handle::eFeatureFetchPolicy_default, CBioseq_Handle::eFeatureFetchPolicy_only_near, CUser_field_Base::GetData(), CUser_object_Base::GetData(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CBioseq_Base_Info::IsSetDescr(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), CSeqdesc_Base::IsUser(), ITERATE, m_FeatureFetchPolicy, str(), CBioseq_Base_Info::x_GetFirstDesc(), CBioseq_Base_Info::x_GetNextDesc(), and CBioseq_Base_Info::x_IsEndDesc().

◆ GetId()

const CBioseq_Info::TId & CBioseq_Info::GetId ( void  ) const

Definition at line 407 of file bioseq_info.cpp.

References m_Id.

Referenced by CMasterSeqSegments::CMasterSeqSegments(), CTSE_ScopeInfo::GetBioseqLock(), CDataLoader::GetExternalAnnotRecords(), CGBDataLoader_Native::GetExternalAnnotRecordsNA(), CPSGDataLoader::GetExternalAnnotRecordsNA(), CDataLoader::GetExternalRecords(), CLDS2_DataLoader::GetExternalRecords(), CGBDataLoader_Native::GetExternalRecords(), CBioseq_Handle::GetId(), CDataLoader::GetIds(), GetSequenceClass(), CDataSource::GetTSESetWithBioseqAnnots(), s_FormatCall(), s_HasMasterId(), CDataSource::x_AddTSEBioseqAnnots(), and CSeq_entry_Info::x_GetBioseqsIds().

◆ GetInst()

const CBioseq_Info::TInst & CBioseq_Info::GetInst ( void  ) const

Definition at line 541 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_assembly, CTSE_Info_Object::fNeedUpdate_seq_data, m_Object, and CTSE_Info_Object::x_Update().

Referenced by CBioseq_Handle::GetInst(), and x_CalcBioseqLength().

◆ GetInst_Ext()

const CBioseq_Info::TInst_Ext & CBioseq_Info::GetInst_Ext ( void  ) const

Definition at line 881 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, m_Object, and CTSE_Info_Object::x_Update().

Referenced by CBioseq_Handle::GetInst_Ext().

◆ GetInst_Fuzz()

const CBioseq_Info::TInst_Fuzz & CBioseq_Info::GetInst_Fuzz ( void  ) const

Definition at line 731 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::GetInst_Fuzz().

◆ GetInst_Hist()

const CBioseq_Info::TInst_Hist & CBioseq_Info::GetInst_Hist ( void  ) const

Definition at line 923 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_assembly, m_Object, and CTSE_Info_Object::x_Update().

Referenced by CBioseq_Handle::GetInst_Hist().

◆ GetInst_Hist_Assembly()

const CBioseq_Info::TInst_Hist_Assembly & CBioseq_Info::GetInst_Hist_Assembly ( void  ) const

Definition at line 966 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_assembly, m_Object, and CTSE_Info_Object::x_Update().

◆ GetInst_Hist_Deleted()

const CBioseq_Info::TInst_Hist_Deleted & CBioseq_Info::GetInst_Hist_Deleted ( void  ) const

Definition at line 1058 of file bioseq_info.cpp.

References m_Object.

◆ GetInst_Hist_Replaced_by()

const CBioseq_Info::TInst_Hist_Replaced_by & CBioseq_Info::GetInst_Hist_Replaced_by ( void  ) const

Definition at line 1029 of file bioseq_info.cpp.

References m_Object.

◆ GetInst_Hist_Replaces()

const CBioseq_Info::TInst_Hist_Replaces & CBioseq_Info::GetInst_Hist_Replaces ( void  ) const

Definition at line 998 of file bioseq_info.cpp.

References m_Object.

◆ GetInst_Length()

CBioseq_Info::TInst_Length CBioseq_Info::GetInst_Length ( void  ) const

Definition at line 676 of file bioseq_info.cpp.

References CSeqMap::GetLength(), m_Object, m_SeqMap, and m_SeqMap_Mtx.

Referenced by GetBioseqLength(), and CBioseq_Handle::GetInst_Length().

◆ GetInst_Mol()

CBioseq_Info::TInst_Mol CBioseq_Info::GetInst_Mol ( void  ) const

Definition at line 633 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::GetInst_Mol(), CDataLoader::GetSequenceType(), CDataSource::x_CollectBioseqs(), and CBioseq_CI::x_IsValidMolType().

◆ GetInst_Repr()

CBioseq_Info::TInst_Repr CBioseq_Info::GetInst_Repr ( void  ) const

Definition at line 591 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::GetInst_Repr().

◆ GetInst_Seq_data()

const CBioseq_Info::TInst_Seq_data & CBioseq_Info::GetInst_Seq_data ( void  ) const

Definition at line 839 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, m_Object, and CTSE_Info_Object::x_Update().

Referenced by CBioseq_Handle::GetInst_Seq_data().

◆ GetInst_Strand()

CBioseq_Info::TInst_Strand CBioseq_Info::GetInst_Strand ( void  ) const

Definition at line 799 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::GetInst_Strand().

◆ GetInst_Topology()

CBioseq_Info::TInst_Topology CBioseq_Info::GetInst_Topology ( void  ) const

Definition at line 765 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::GetInst_Topology().

◆ GetSeqMap()

const CSeqMap & CBioseq_Info::GetSeqMap ( void  ) const

Definition at line 1245 of file bioseq_info.cpp.

References CSeqMap::CreateSeqMapForBioseq(), CSeqMap::m_Bioseq, m_Object, m_SeqMap, and m_SeqMap_Mtx.

Referenced by CMasterSeqSegments::CMasterSeqSegments(), CBioseq_Handle::GetSeqMap(), and CTSE_Default_Assigner::LoadSequence().

◆ GetSequenceClass()

int CBioseq_Info::GetSequenceClass ( void  ) const

Definition at line 1277 of file bioseq_info.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Other, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CBioseq_Handle::eSequenceClass_INSD, CBioseq_Handle::eSequenceClass_none, CBioseq_Handle::eSequenceClass_REFSEQ, CBioseq_Handle::eSequenceClass_TPA, GetId(), and ITERATE.

Referenced by CSeqMap::x_GetSequenceClass().

◆ GetTaxId()

TTaxId CBioseq_Info::GetTaxId ( void  ) const

Definition at line 1256 of file bioseq_info.cpp.

References CSeqdesc_Base::e_Org, CSeqdesc_Base::e_Source, COrg_ref::GetTaxId(), CBioseq_Base_Info::x_SearchFirstDesc(), and ZERO_TAX_ID.

Referenced by CDataLoader::GetTaxId().

◆ HasId()

bool CBioseq_Info::HasId ( const CSeq_id_Handle &  id) const

Definition at line 425 of file bioseq_info.cpp.

References m_Id.

◆ IdString()

string CBioseq_Info::IdString ( void  ) const

Definition at line 1221 of file bioseq_info.cpp.

References ITERATE, and m_Id.

◆ IsAa()

bool CBioseq_Info::IsAa ( void  ) const

Definition at line 1076 of file bioseq_info.cpp.

References m_Object.

◆ IsNa()

bool CBioseq_Info::IsNa ( void  ) const

Definition at line 1070 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_CI::x_IsValidMolType().

◆ IsSetId()

bool CBioseq_Info::IsSetId ( void  ) const

Definition at line 395 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::IsSetId().

◆ IsSetInst()

bool CBioseq_Info::IsSetInst ( void  ) const

Definition at line 529 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_Handle::IsSetInst(), IsSetInst_Ext(), IsSetInst_Fuzz(), IsSetInst_Hist(), IsSetInst_Length(), IsSetInst_Mol(), IsSetInst_Repr(), IsSetInst_Seq_data(), IsSetInst_Strand(), IsSetInst_Topology(), and ResetInst().

◆ IsSetInst_Ext()

bool CBioseq_Info::IsSetInst_Ext ( void  ) const

Definition at line 869 of file bioseq_info.cpp.

References IsSetInst(), and m_Object.

Referenced by CanGetInst_Ext(), CBioseq_Handle::IsSetInst_Ext(), and ResetInst_Ext().

◆ IsSetInst_Fuzz()

bool CBioseq_Info::IsSetInst_Fuzz ( void  ) const

Definition at line 719 of file bioseq_info.cpp.

References IsSetInst(), and m_Object.

Referenced by CBioseq_Handle::IsSetInst_Fuzz(), and ResetInst_Fuzz().

◆ IsSetInst_Hist()

bool CBioseq_Info::IsSetInst_Hist ( void  ) const

Definition at line 911 of file bioseq_info.cpp.

References IsSetInst(), and m_Object.

Referenced by CBioseq_Handle::IsSetInst_Hist(), IsSetInst_Hist_Assembly(), IsSetInst_Hist_Deleted(), IsSetInst_Hist_Replaced_by(), IsSetInst_Hist_Replaces(), and ResetInst_Hist().

◆ IsSetInst_Hist_Assembly()

bool CBioseq_Info::IsSetInst_Hist_Assembly ( void  ) const

Definition at line 952 of file bioseq_info.cpp.

References IsSetInst_Hist(), m_AssemblyChunk, and m_Object.

◆ IsSetInst_Hist_Deleted()

bool CBioseq_Info::IsSetInst_Hist_Deleted ( void  ) const

Definition at line 1045 of file bioseq_info.cpp.

References IsSetInst_Hist(), and m_Object.

◆ IsSetInst_Hist_Replaced_by()

bool CBioseq_Info::IsSetInst_Hist_Replaced_by ( void  ) const

Definition at line 1014 of file bioseq_info.cpp.

References IsSetInst_Hist(), and m_Object.

◆ IsSetInst_Hist_Replaces()

bool CBioseq_Info::IsSetInst_Hist_Replaces ( void  ) const

Definition at line 985 of file bioseq_info.cpp.

References IsSetInst_Hist(), and m_Object.

◆ IsSetInst_Length()

bool CBioseq_Info::IsSetInst_Length ( void  ) const

Definition at line 664 of file bioseq_info.cpp.

References IsSetInst(), and m_Object.

Referenced by GetBioseqLength(), CBioseq_Handle::IsSetInst_Length(), and ResetInst_Length().

◆ IsSetInst_Mol()

bool CBioseq_Info::IsSetInst_Mol ( void  ) const

Definition at line 621 of file bioseq_info.cpp.

References IsSetInst(), and m_Object.

Referenced by CBioseq_Handle::IsSetInst_Mol(), and ResetInst_Mol().

◆ IsSetInst_Repr()

bool CBioseq_Info::IsSetInst_Repr ( void  ) const

Definition at line 579 of file bioseq_info.cpp.

References IsSetInst(), and m_Object.

Referenced by CBioseq_Handle::IsSetInst_Repr(), and ResetInst_Repr().

◆ IsSetInst_Seq_data()

bool CBioseq_Info::IsSetInst_Seq_data ( void  ) const

Definition at line 822 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, IsSetInst(), m_Object, m_Seq_dataChunks, and CTSE_Info_Object::x_NeedUpdate().

Referenced by CanGetInst_Seq_data(), CBioseq_Handle::IsSetInst_Seq_data(), and ResetInst_Seq_data().

◆ IsSetInst_Strand()

bool CBioseq_Info::IsSetInst_Strand ( void  ) const

Definition at line 787 of file bioseq_info.cpp.

References IsSetInst(), and m_Object.

Referenced by CBioseq_Handle::IsSetInst_Strand(), and ResetInst_Strand().

◆ IsSetInst_Topology()

bool CBioseq_Info::IsSetInst_Topology ( void  ) const

Definition at line 753 of file bioseq_info.cpp.

References IsSetInst(), and m_Object.

Referenced by CBioseq_Handle::IsSetInst_Topology(), and ResetInst_Topology().

◆ operator=()

CBioseq_Info& CBioseq_Info::operator= ( const CBioseq_Info &  )
private

◆ RemoveId()

bool CBioseq_Info::RemoveId ( const CSeq_id_Handle &  id)

Definition at line 447 of file bioseq_info.cpp.

References CTSE_Info_Object::GetBioObjectId(), CSeq_id_Handle::GetHandle(), CTSE_Info_Object::GetTSE_Info(), m_Id, m_IdChangeCounter, m_Object, NON_CONST_ITERATE, CTSE_Info_Object::SetBioObjectId(), and CTSE_Info::x_ResetBioseqId().

Referenced by x_ApplyCmd().

◆ ResetId()

void CBioseq_Info::ResetId ( void  )

Definition at line 413 of file bioseq_info.cpp.

References CTSE_Info_Object::GetTSE_Info(), ITERATE, m_Id, m_IdChangeCounter, m_Object, CTSE_Info_Object::SetBioObjectId(), and CTSE_Info::x_ResetBioseqId().

Referenced by x_ApplyCmd().

◆ ResetInst()

void CBioseq_Info::ResetInst ( void  )

Definition at line 555 of file bioseq_info.cpp.

References IsSetInst(), m_Object, m_Seq_dataChunks, and x_ResetSeqMap().

Referenced by CBioseq_EditHandle::x_RealResetInst().

◆ ResetInst_Ext()

void CBioseq_Info::ResetInst_Ext ( )

Definition at line 896 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, IsSetInst_Ext(), m_Object, m_Seq_dataChunks, x_ResetSeqMap(), and CTSE_Info_Object::x_Update().

Referenced by CBioseq_EditHandle::x_RealResetInst_Ext().

◆ ResetInst_Fuzz()

void CBioseq_Info::ResetInst_Fuzz ( )

Definition at line 742 of file bioseq_info.cpp.

References IsSetInst_Fuzz(), and m_Object.

Referenced by CBioseq_EditHandle::x_RealResetInst_Fuzz().

◆ ResetInst_Hist()

void CBioseq_Info::ResetInst_Hist ( )

Definition at line 938 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_assembly, IsSetInst_Hist(), m_AssemblyChunk, m_Object, and CTSE_Info_Object::x_Update().

Referenced by CBioseq_EditHandle::x_RealResetInst_Hist().

◆ ResetInst_Length()

void CBioseq_Info::ResetInst_Length ( )

Definition at line 695 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, IsSetInst_Length(), m_Object, x_ResetSeqMap(), and CTSE_Info_Object::x_Update().

Referenced by CBioseq_EditHandle::x_RealResetInst_Length().

◆ ResetInst_Mol()

void CBioseq_Info::ResetInst_Mol ( )

Definition at line 648 of file bioseq_info.cpp.

References IsSetInst_Mol(), m_Object, m_SeqMap, m_SeqMap_Mtx, and CSeqMap::ResetMol().

Referenced by CBioseq_EditHandle::x_RealResetInst_Mol().

◆ ResetInst_Repr()

void CBioseq_Info::ResetInst_Repr ( )

Definition at line 606 of file bioseq_info.cpp.

References IsSetInst_Repr(), m_Object, m_SeqMap, m_SeqMap_Mtx, and CSeqMap::ResetRepr().

Referenced by CBioseq_EditHandle::x_RealResetInst_Repr().

◆ ResetInst_Seq_data()

void CBioseq_Info::ResetInst_Seq_data ( )

Definition at line 854 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, IsSetInst_Seq_data(), m_Object, m_Seq_dataChunks, x_ResetSeqMap(), and CTSE_Info_Object::x_Update().

Referenced by CBioseq_EditHandle::x_RealResetInst_Seq_data().

◆ ResetInst_Strand()

void CBioseq_Info::ResetInst_Strand ( )

Definition at line 810 of file bioseq_info.cpp.

References IsSetInst_Strand(), and m_Object.

Referenced by CBioseq_EditHandle::x_RealResetInst_Strand().

◆ ResetInst_Topology()

void CBioseq_Info::ResetInst_Topology ( )

Definition at line 776 of file bioseq_info.cpp.

References IsSetInst_Topology(), and m_Object.

Referenced by CBioseq_EditHandle::x_RealResetInst_Topology().

◆ SetInst()

void CBioseq_Info::SetInst ( TInst &  v)

Definition at line 548 of file bioseq_info.cpp.

References m_Object, m_Seq_dataChunks, and x_ResetSeqMap().

Referenced by CBioseq_EditHandle::x_RealSetInst().

◆ SetInst_Ext()

void CBioseq_Info::SetInst_Ext ( TInst_Ext &  v)

Definition at line 888 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, m_Object, m_Seq_dataChunks, x_ResetSeqMap(), and CTSE_Info_Object::x_Update().

Referenced by CBioseq_EditHandle::x_RealSetInst_Ext().

◆ SetInst_Fuzz()

void CBioseq_Info::SetInst_Fuzz ( TInst_Fuzz &  v)

Definition at line 737 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_EditHandle::x_RealSetInst_Fuzz().

◆ SetInst_Hist()

void CBioseq_Info::SetInst_Hist ( TInst_Hist &  v)

Definition at line 930 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_assembly, m_AssemblyChunk, m_Object, and CTSE_Info_Object::x_Update().

Referenced by CBioseq_EditHandle::x_RealSetInst_Hist().

◆ SetInst_Hist_Assembly()

void CBioseq_Info::SetInst_Hist_Assembly ( const TInst_Hist_Assembly &  v)

Definition at line 973 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_assembly, m_AssemblyChunk, m_Object, and CTSE_Info_Object::x_Update().

Referenced by CTSE_Default_Assigner::LoadAssembly().

◆ SetInst_Hist_Deleted()

void CBioseq_Info::SetInst_Hist_Deleted ( TInst_Hist_Deleted &  v)

Definition at line 1064 of file bioseq_info.cpp.

References m_Object.

◆ SetInst_Hist_Replaced_by()

void CBioseq_Info::SetInst_Hist_Replaced_by ( TInst_Hist_Replaced_by &  v)

Definition at line 1035 of file bioseq_info.cpp.

References m_Object.

◆ SetInst_Hist_Replaces()

void CBioseq_Info::SetInst_Hist_Replaces ( TInst_Hist_Replaces &  v)

Definition at line 1004 of file bioseq_info.cpp.

References m_Object.

◆ SetInst_Length()

void CBioseq_Info::SetInst_Length ( TInst_Length  v)

Definition at line 688 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, m_Object, x_ResetSeqMap(), and CTSE_Info_Object::x_Update().

Referenced by CBioseq_EditHandle::x_RealSetInst_Length().

◆ SetInst_Mol()

void CBioseq_Info::SetInst_Mol ( TInst_Mol  v)

Definition at line 639 of file bioseq_info.cpp.

References m_Object, m_SeqMap, m_SeqMap_Mtx, and CSeqMap::SetMol().

Referenced by CBioseq_EditHandle::x_RealSetInst_Mol().

◆ SetInst_Repr()

void CBioseq_Info::SetInst_Repr ( TInst_Repr  v)

Definition at line 597 of file bioseq_info.cpp.

References m_Object, m_SeqMap, m_SeqMap_Mtx, and CSeqMap::SetRepr().

Referenced by CBioseq_EditHandle::x_RealSetInst_Repr().

◆ SetInst_Seq_data()

void CBioseq_Info::SetInst_Seq_data ( TInst_Seq_data &  v)

Definition at line 846 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, m_Object, m_Seq_dataChunks, x_ResetSeqMap(), and CTSE_Info_Object::x_Update().

Referenced by CBioseq_EditHandle::x_RealSetInst_Seq_data().

◆ SetInst_Strand()

void CBioseq_Info::SetInst_Strand ( TInst_Strand  v)

Definition at line 805 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_EditHandle::x_RealSetInst_Strand().

◆ SetInst_Topology()

void CBioseq_Info::SetInst_Topology ( TInst_Topology  v)

Definition at line 771 of file bioseq_info.cpp.

References m_Object.

Referenced by CBioseq_EditHandle::x_RealSetInst_Topology().

◆ sx_ShallowCopy() [1/2]

CRef< CSeq_inst > CBioseq_Info::sx_ShallowCopy ( const TInst &  inst)
staticprivate

Definition at line 357 of file bioseq_info.cpp.

References CSeq_inst_Base::GetExt(), CSeq_inst_Base::GetFuzz(), CSeq_inst_Base::GetHist(), CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetMol(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::GetSeq_data(), CSeq_inst_Base::GetStrand(), CSeq_inst_Base::GetTopology(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetFuzz(), CSeq_inst_Base::IsSetHist(), CSeq_inst_Base::IsSetLength(), CSeq_inst_Base::IsSetMol(), CSeq_inst_Base::IsSetRepr(), CSeq_inst_Base::IsSetSeq_data(), CSeq_inst_Base::IsSetStrand(), and CSeq_inst_Base::IsSetTopology().

◆ sx_ShallowCopy() [2/2]

CRef< CBioseq > CBioseq_Info::sx_ShallowCopy ( const TObject &  obj)
staticprivate

Definition at line 337 of file bioseq_info.cpp.

References CSeq_descr_Base::Get(), CBioseq_Base::GetAnnot(), CBioseq_Base::GetDescr(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CBioseq_Base::IsSetAnnot(), CBioseq_Base::IsSetDescr(), CBioseq_Base::IsSetId(), and CBioseq_Base::IsSetInst().

Referenced by x_SetObject().

◆ x_AddAssemblyChunkId()

void CBioseq_Info::x_AddAssemblyChunkId ( TChunkId  chunk_id)

Definition at line 146 of file bioseq_info.cpp.

References _ASSERT, CTSE_Info_Object::fNeedUpdate_assembly, m_AssemblyChunk, and CTSE_Info_Object::x_SetNeedUpdate().

Referenced by CTSE_Default_Assigner::AddAssemblyInfo().

◆ x_AddSeq_dataChunkId()

void CBioseq_Info::x_AddSeq_dataChunkId ( TChunkId  chunk_id)

Definition at line 139 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, m_Seq_dataChunks, and CTSE_Info_Object::x_SetNeedUpdate().

◆ x_AttachMap()

void CBioseq_Info::x_AttachMap ( CSeqMap &  seq_map)

Definition at line 1233 of file bioseq_info.cpp.

References CSeqMap::m_Bioseq, m_SeqMap, m_SeqMap_Mtx, NCBI_THROW, and CRef< C, Locker >::Reset().

◆ x_CalcBioseqLength() [1/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CDelta_ext &  delta) const
private

Definition at line 1196 of file bioseq_info.cpp.

References delta(), ITERATE, and x_CalcBioseqLength().

◆ x_CalcBioseqLength() [2/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CDelta_seq &  delta_seq) const
private

Definition at line 1206 of file bioseq_info.cpp.

References CDelta_seq_Base::e_Literal, CDelta_seq_Base::e_Loc, CSeq_literal_Base::GetLength(), CDelta_seq_Base::GetLiteral(), CDelta_seq_Base::GetLoc(), NCBI_THROW, CDelta_seq_Base::Which(), and x_CalcBioseqLength().

◆ x_CalcBioseqLength() [3/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CPacked_seqint &  ints) const
private

Definition at line 1127 of file bioseq_info.cpp.

References CPacked_seqint_Base::Get(), and ITERATE.

◆ x_CalcBioseqLength() [4/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CSeg_ext &  seg_ext) const
private

Definition at line 1186 of file bioseq_info.cpp.

References CSeg_ext_Base::Get(), ITERATE, and x_CalcBioseqLength().

◆ x_CalcBioseqLength() [5/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CSeq_id &  whole) const
private

Definition at line 1114 of file bioseq_info.cpp.

References CTSE_Info::FindMatchingBioseq(), GetBioseqLength(), CSeq_id_Handle::GetHandle(), CTSE_Info_Object::GetTSE_Info(), NCBI_THROW, and whole.

◆ x_CalcBioseqLength() [6/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CSeq_inst &  inst) const
private

Definition at line 1092 of file bioseq_info.cpp.

References CSeq_ext_Base::e_Delta, CSeq_ext_Base::e_Ref, CSeq_ext_Base::e_Seg, CRef_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CSeq_ext_Base::GetRef(), CSeq_ext_Base::GetSeg(), CSeq_inst_Base::IsSetExt(), NCBI_THROW, CSeq_ext_Base::Which(), and x_CalcBioseqLength().

◆ x_CalcBioseqLength() [7/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CSeq_loc &  seq_loc) const
private

Definition at line 1137 of file bioseq_info.cpp.

References CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_Base::GetEquiv(), CSeq_loc_Base::GetInt(), CSeq_interval::GetLength(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CPacked_seqpnt_Base::GetPoints(), CSeq_loc_Base::GetWhole(), NCBI_THROW, CSeq_loc_Base::Which(), and x_CalcBioseqLength().

◆ x_CalcBioseqLength() [8/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CSeq_loc_equiv &  seq_equiv) const
private

Definition at line 1176 of file bioseq_info.cpp.

References CSeq_loc_equiv_Base::Get(), ITERATE, and x_CalcBioseqLength().

◆ x_CalcBioseqLength() [9/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( const CSeq_loc_mix &  seq_mix) const
private

Definition at line 1166 of file bioseq_info.cpp.

References CSeq_loc_mix_Base::Get(), ITERATE, and x_CalcBioseqLength().

◆ x_CalcBioseqLength() [10/10]

TSeqPos CBioseq_Info::x_CalcBioseqLength ( void  ) const
private

Definition at line 1086 of file bioseq_info.cpp.

References GetInst().

Referenced by GetBioseqLength(), and x_CalcBioseqLength().

◆ x_CanGetDescr()

bool CBioseq_Info::x_CanGetDescr ( void  ) const
virtual

Implements CBioseq_Base_Info.

Definition at line 479 of file bioseq_info.cpp.

References m_Object.

◆ x_DoUpdate()

void CBioseq_Info::x_DoUpdate ( TNeedUpdateFlags  flags)
virtual

Reimplemented from CBioseq_Base_Info.

Definition at line 155 of file bioseq_info.cpp.

References flags, CTSE_Info_Object::fNeedUpdate_assembly, CTSE_Info_Object::fNeedUpdate_seq_data, m_AssemblyChunk, m_Object, m_Seq_dataChunks, m_SeqMap, m_SeqMap_Mtx, CBioseq_Base_Info::x_DoUpdate(), CTSE_Info_Object::x_LoadChunk(), CTSE_Info_Object::x_LoadChunks(), and CSeqMap::x_UpdateSeq_inst().

◆ x_DSAttachContents()

void CBioseq_Info::x_DSAttachContents ( CDataSource &  ds)
privatevirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 176 of file bioseq_info.cpp.

References m_Object, CBioseq_Base_Info::x_DSAttachContents(), and x_DSMapObject().

◆ x_DSDetachContents()

void CBioseq_Info::x_DSDetachContents ( CDataSource &  ds)
privatevirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 183 of file bioseq_info.cpp.

References m_Object, CBioseq_Base_Info::x_DSDetachContents(), and x_DSUnmapObject().

◆ x_DSMapObject()

void CBioseq_Info::x_DSMapObject ( CConstRef< TObject >  obj,
CDataSource &  ds 
)
private

Definition at line 190 of file bioseq_info.cpp.

References CDataSource::x_Map().

Referenced by x_DSAttachContents(), and x_SetObject().

◆ x_DSUnmapObject()

void CBioseq_Info::x_DSUnmapObject ( CConstRef< TObject >  obj,
CDataSource &  ds 
)
private

Definition at line 196 of file bioseq_info.cpp.

References CDataSource::x_Unmap().

Referenced by x_DSDetachContents().

◆ x_GetDescr()

const CSeq_descr & CBioseq_Info::x_GetDescr ( void  ) const
virtual

Implements CBioseq_Base_Info.

Definition at line 485 of file bioseq_info.cpp.

References m_Object.

◆ x_GetObject() [1/2]

CBioseq & CBioseq_Info::x_GetObject ( void  )
inlineprivate

Definition at line 311 of file bioseq_info.hpp.

References m_Object.

◆ x_GetObject() [2/2]

const CBioseq & CBioseq_Info::x_GetObject ( void  ) const
inlineprivate

Definition at line 318 of file bioseq_info.hpp.

References m_Object.

◆ x_IsSetDescr()

bool CBioseq_Info::x_IsSetDescr ( void  ) const
virtual

Implements CBioseq_Base_Info.

Definition at line 473 of file bioseq_info.cpp.

References m_Object.

◆ x_ParentAttach()

void CBioseq_Info::x_ParentAttach ( CSeq_entry_Info &  parent)
privatevirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 224 of file bioseq_info.cpp.

References _ASSERT, CSeq_entry_Base::GetSeq(), m_Object, CSeq_entry::ParentizeOneLevel(), CSeq_entry_Info::x_GetObject(), and CBioseq_Base_Info::x_ParentAttach().

◆ x_ParentDetach()

void CBioseq_Info::x_ParentDetach ( CSeq_entry_Info &  parent)
privatevirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 236 of file bioseq_info.cpp.

References CBioseq_Base_Info::x_ParentDetach().

◆ x_ResetDescr()

void CBioseq_Info::x_ResetDescr ( void  )
virtual

Implements CBioseq_Base_Info.

Definition at line 503 of file bioseq_info.cpp.

References m_Object.

◆ x_ResetObjAnnot()

void CBioseq_Info::x_ResetObjAnnot ( void  )
protectedvirtual

Implements CBioseq_Base_Info.

Definition at line 519 of file bioseq_info.cpp.

References m_Object.

◆ x_ResetSeqMap()

void CBioseq_Info::x_ResetSeqMap ( void  )
protected

Definition at line 565 of file bioseq_info.cpp.

References CSeqMap::m_Bioseq, m_SeqMap, m_SeqMap_Mtx, and CRef< C, Locker >::Reset().

Referenced by ResetInst(), ResetInst_Ext(), ResetInst_Length(), ResetInst_Seq_data(), SetInst(), SetInst_Ext(), SetInst_Length(), SetInst_Seq_data(), and ~CBioseq_Info().

◆ x_SetChangedSeqMap()

void CBioseq_Info::x_SetChangedSeqMap ( void  )
protected

Definition at line 133 of file bioseq_info.cpp.

References CTSE_Info_Object::fNeedUpdate_seq_data, and CTSE_Info_Object::x_SetNeedUpdate().

Referenced by CSeqMap::x_SetChanged().

◆ x_SetDescr() [1/2]

void CBioseq_Info::x_SetDescr ( TDescr &  v)
virtual

Implements CBioseq_Base_Info.

Definition at line 497 of file bioseq_info.cpp.

References m_Object.

◆ x_SetDescr() [2/2]

CSeq_descr & CBioseq_Info::x_SetDescr ( void  )
virtual

Implements CBioseq_Base_Info.

Definition at line 491 of file bioseq_info.cpp.

References m_Object.

Referenced by AddMasterDescr().

◆ x_SetObjAnnot()

CBioseq::TAnnot & CBioseq_Info::x_SetObjAnnot ( void  )
protectedvirtual

Implements CBioseq_Base_Info.

Definition at line 513 of file bioseq_info.cpp.

References m_Object.

◆ x_SetObject() [1/2]

void CBioseq_Info::x_SetObject ( const CBioseq_Info &  info,
TObjectCopyMap *  copy_map 
)
private

Definition at line 312 of file bioseq_info.cpp.

References _ASSERT, CTSE_Info_Object::GetDataSource(), CTSE_Info_Object::HasDataSource(), info, CSeqMap::m_Bioseq, m_FeatureFetchPolicy, m_Id, m_Object, m_SeqMap, m_SeqMap_Mtx, sx_ShallowCopy(), x_DSMapObject(), and CBioseq_Base_Info::x_SetAnnot().

◆ x_SetObject() [2/2]

void CBioseq_Info::x_SetObject ( TObject &  obj)
private

Definition at line 292 of file bioseq_info.cpp.

References _ASSERT, CTSE_Info_Object::GetDataSource(), CSeq_id_Handle::GetHandle(), CBioseq_Base::GetId(), CTSE_Info_Object::HasDataSource(), CBioseq_Base::IsSetAnnot(), CBioseq_Base::IsSetId(), ITERATE, m_FeatureFetchPolicy, m_Id, m_Object, CRef< C, Locker >::Reset(), x_DSMapObject(), and CBioseq_Base_Info::x_SetAnnot().

Referenced by CBioseq_Info().

◆ x_TSEAttachContents()

void CBioseq_Info::x_TSEAttachContents ( CTSE_Info &  tse)
privatevirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 202 of file bioseq_info.cpp.

References CTSE_Info_Object::SetBioObjectId(), CTSE_Info::x_IndexBioseq(), and CBioseq_Base_Info::x_TSEAttachContents().

◆ x_TSEDetachContents()

void CBioseq_Info::x_TSEDetachContents ( CTSE_Info &  tse)
privatevirtual

Reimplemented from CBioseq_Base_Info.

Definition at line 215 of file bioseq_info.cpp.

References ITERATE, m_Id, CTSE_Info::x_ResetBioseqId(), and CBioseq_Base_Info::x_TSEDetachContents().

Friends And Related Function Documentation

◆ CBioseq_set_Info

friend class CBioseq_set_Info
friend

Definition at line 241 of file bioseq_info.hpp.

◆ CDataSource

friend class CDataSource
friend

Definition at line 236 of file bioseq_info.hpp.

◆ CScope_Impl

friend class CScope_Impl
friend

Definition at line 237 of file bioseq_info.hpp.

◆ CSeq_entry_Info

friend class CSeq_entry_Info
friend

Definition at line 240 of file bioseq_info.hpp.

◆ CSeqMap

friend class CSeqMap
friend

Definition at line 242 of file bioseq_info.hpp.

◆ CTSE_Info

friend class CTSE_Info
friend

Definition at line 239 of file bioseq_info.hpp.

Member Data Documentation

◆ m_AssemblyChunk

TChunkId CBioseq_Info::m_AssemblyChunk
private

Definition at line 296 of file bioseq_info.hpp.

Referenced by CBioseq_Info(), IsSetInst_Hist_Assembly(), ResetInst_Hist(), SetInst_Hist(), SetInst_Hist_Assembly(), x_AddAssemblyChunkId(), and x_DoUpdate().

◆ m_FeatureFetchPolicy

int CBioseq_Info::m_FeatureFetchPolicy
mutableprivate

Definition at line 297 of file bioseq_info.hpp.

Referenced by GetFeatureFetchPolicy(), and x_SetObject().

◆ m_Id

TId CBioseq_Info::m_Id
private

Definition at line 289 of file bioseq_info.hpp.

Referenced by AddId(), GetId(), HasId(), IdString(), RemoveId(), ResetId(), x_SetObject(), and x_TSEDetachContents().

◆ m_IdChangeCounter

atomic<int> CBioseq_Info::m_IdChangeCounter
private

Definition at line 298 of file bioseq_info.hpp.

Referenced by AddId(), RemoveId(), ResetId(), and CScope_Impl::x_GetTSESetWithAnnots().

◆ m_Object

CRef<TObject> CBioseq_Info::m_Object
private

Definition at line 286 of file bioseq_info.hpp.

Referenced by AddId(), CanGetId(), CanGetInst(), CanGetInst_Fuzz(), CanGetInst_Hist(), CanGetInst_Hist_Deleted(), CanGetInst_Hist_Replaced_by(), CanGetInst_Hist_Replaces(), CanGetInst_Length(), CanGetInst_Mol(), CanGetInst_Repr(), CanGetInst_Strand(), CanGetInst_Topology(), GetBioseqCore(), GetCompleteBioseq(), GetInst(), GetInst_Ext(), GetInst_Fuzz(), GetInst_Hist(), GetInst_Hist_Assembly(), GetInst_Hist_Deleted(), GetInst_Hist_Replaced_by(), GetInst_Hist_Replaces(), GetInst_Length(), GetInst_Mol(), GetInst_Repr(), GetInst_Seq_data(), GetInst_Strand(), GetInst_Topology(), GetSeqMap(), IsAa(), IsNa(), IsSetId(), IsSetInst(), IsSetInst_Ext(), IsSetInst_Fuzz(), IsSetInst_Hist(), IsSetInst_Hist_Assembly(), IsSetInst_Hist_Deleted(), IsSetInst_Hist_Replaced_by(), IsSetInst_Hist_Replaces(), IsSetInst_Length(), IsSetInst_Mol(), IsSetInst_Repr(), IsSetInst_Seq_data(), IsSetInst_Strand(), IsSetInst_Topology(), RemoveId(), ResetId(), ResetInst(), ResetInst_Ext(), ResetInst_Fuzz(), ResetInst_Hist(), ResetInst_Length(), ResetInst_Mol(), ResetInst_Repr(), ResetInst_Seq_data(), ResetInst_Strand(), ResetInst_Topology(), SetInst(), SetInst_Ext(), SetInst_Fuzz(), SetInst_Hist(), SetInst_Hist_Assembly(), SetInst_Hist_Deleted(), SetInst_Hist_Replaced_by(), SetInst_Hist_Replaces(), SetInst_Length(), SetInst_Mol(), SetInst_Repr(), SetInst_Seq_data(), SetInst_Strand(), SetInst_Topology(), x_CanGetDescr(), x_DoUpdate(), x_DSAttachContents(), x_DSDetachContents(), x_GetDescr(), x_GetObject(), x_IsSetDescr(), x_ParentAttach(), x_ResetDescr(), x_ResetObjAnnot(), x_SetDescr(), x_SetObjAnnot(), and x_SetObject().

◆ m_Seq_dataChunks

TChunkIds CBioseq_Info::m_Seq_dataChunks
private

Definition at line 295 of file bioseq_info.hpp.

Referenced by CBioseq_Info(), IsSetInst_Seq_data(), ResetInst(), ResetInst_Ext(), ResetInst_Seq_data(), SetInst(), SetInst_Ext(), SetInst_Seq_data(), x_AddSeq_dataChunkId(), and x_DoUpdate().

◆ m_SeqMap

CRef<CSeqMap> CBioseq_Info::m_SeqMap
mutableprivate

Definition at line 292 of file bioseq_info.hpp.

Referenced by GetInst_Length(), GetSeqMap(), ResetInst_Mol(), ResetInst_Repr(), SetInst_Mol(), SetInst_Repr(), x_AttachMap(), x_DoUpdate(), x_ResetSeqMap(), and x_SetObject().

◆ m_SeqMap_Mtx

CFastMutex CBioseq_Info::m_SeqMap_Mtx
mutableprivate

Definition at line 293 of file bioseq_info.hpp.

Referenced by GetInst_Length(), GetSeqMap(), ResetInst_Mol(), ResetInst_Repr(), SetInst_Mol(), SetInst_Repr(), x_AttachMap(), x_DoUpdate(), x_ResetSeqMap(), and x_SetObject().

The documentation for this class was generated from the following files:
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Modified on Sat Dec 02 09:21:51 2023 by modify_doxy.py rev. 669887