#include <objmgr/scope.hpp>

Inheritance diagram for CScope:

Collaboration diagram for CScope:

Public Types
enum	EPriority { kPriority_Default = -1 , kPriority_NotSet = -1 }

enum	EGetBioseqFlag { eGetBioseq_Resolved , eGetBioseq_Loaded , eGetBioseq_All }

enum	EMissing { eMissing_Throw , eMissing_Null , eMissing_Default = eMissing_Throw }
	GetXxxHandle control values. More...

enum	EExist { eExist_Throw , eExist_Get , eExist_Default = eExist_Throw }
	AddXxx() control values. More...

enum	EActionIfLocked { eKeepIfLocked , eThrowIfLocked , eRemoveIfLocked }

enum	ERemoveDataLoaders { eRemoveDataLoaders }
	Clear all information in the scope including data loaders. More...

enum	EForceLoad { eNoForceLoad , eForceLoad }
	EForceLoad flag instruct scope to ignore already loaded information and always request data loader for data. More...

enum	EGetFlags { fForceLoad = (1 << 0) , fThrowOnMissingSequence = (1 << 1) , fThrowOnMissingData = (1 << 2) , fThrowOnMissing = fThrowOnMissingSequence\|fThrowOnMissingData , fDoNotRecalculate = (1 << 3) }
	Flags to control behavior of various meta-data getters fForceLoad instructs scope to ignore already loaded information and alway request data loader for data fThrowOnMissing instructs to throw an exeption if the requested data is missing - either sequence id cannot be found in any data loader or the sequence doesn't have the requested meta-data without the flag getter will return special value. More...

enum	EForceLabelLoad { eNoForceLabelLoad = eNoForceLoad , eForceLabelLoad = eForceLoad }
	obsolete enum More...

enum	ETSEKind { eManualTSEs , eAllTSEs }

typedef int	TPriority
	priority type and special value for added objects More...

typedef vector< CSeq_id_Handle >	TIds

typedef vector< CBioseq_Handle >	TBioseqHandles

typedef vector< CTSE_Handle >	TCDD_Entries
	Get CDD annotations for all ids. More...

typedef CBlobIdKey	TBlobId

typedef int	TGetFlags

typedef int	TSequenceHash
	Get sequence data hash value Return 0 if sequence is not found or if its hash is not known Note: 0 can be a real hash value, use flags to distinguish these cases. More...

typedef vector< CSeq_id_Handle >	TSeq_id_Handles
	Bulk retrieval methods Common argument typedef - vector of requested ids. More...

typedef vector< TIds >	TBulkIds
	Get all ids of sequences Returns empty ids if the sequence is not found. More...

typedef vector< TGi >	TGIs
	Get GI of a sequence Returns ZERO_GI for sequence that aren't found or don't have GI. More...

typedef vector< string >	TLabels
	Get short descriptions of sequences, usually "accession.version" Returns empty strings for sequences that aren't found. More...

typedef vector< TTaxId >	TTaxIds
	Get taxonomy ids of sequences Return -1 for sequences that aren't found Return 0 for sequences that don't have taxonomy id. More...

typedef vector< TSeqPos >	TSequenceLengths
	Get lengths of sequences Return kInvalidSeqPos for sequences that aren't found. More...

typedef vector< CSeq_inst::TMol >	TSequenceTypes
	Get molecular types of sequences (protein/dna/rna) Return CSeq_inst::eMol_not_set for sequences that aren't found. More...

typedef vector< CBioseq_Handle::TBioseqStateFlags >	TSequenceStates
	Get GenBank states of sequences Return (fState_not_found\|fState_no_data) for sequences that aren't found. More...

typedef vector< TSequenceHash >	TSequenceHashes
	Get data hashes of sequences Return 0 for sequences that aren't found or they don't have hash Note: 0 can be a real hash value, use flags to distinguish these cases. More...

typedef vector< CSeq_entry_Handle >	TTSE_Handles

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
	CScope (CObjectManager &objmgr)

virtual	~CScope (void)

CObjectManager &	GetObjectManager (void)
	Get object manager controlling this scope. More...

CBioseq_Handle	GetBioseqHandle (const CSeq_id &id)
	Get bioseq handle by seq-id. More...

CBioseq_Handle	GetBioseqHandle (const CSeq_id_Handle &id)
	Get bioseq handle by seq-id handle. More...

CBioseq_Handle	GetBioseqHandle (const CSeq_loc &loc)
	Get bioseq handle by seq-loc. More...

CBioseq_Handle	GetBioseqHandle (const CSeq_id &id, EGetBioseqFlag get_flag)
	Get bioseq handle without loading new data. More...

CBioseq_Handle	GetBioseqHandle (const CSeq_id_Handle &id, EGetBioseqFlag get_flag)
	Get bioseq handle without loading new data. More...

bool	IsSameBioseq (const CSeq_id_Handle &id1, const CSeq_id_Handle &id2, EGetBioseqFlag get_flag)
	Check if two seq-ids are resolved to the same Bioseq. More...

TBioseqHandles	GetBioseqHandles (const TIds &ids)
	Get bioseq handles for all ids. More...

TCDD_Entries	GetCDDAnnots (const TIds &idhs)

TCDD_Entries	GetCDDAnnots (const TBioseqHandles &bhs)

CSeq_entry_Handle	GetSeq_entryHandle (CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)
	Get Seq-entry handle by its blob-id, with possible loading. More...

CTSE_Handle	GetTSE_Handle (const CSeq_entry &tse, EMissing action=eMissing_Default)
	Find object in scope If object is not found GetXxxHandle() methods will either throw an exception or return null handle depending on argument. More...

CBioseq_Handle	GetBioseqHandle (const CBioseq &bioseq, EMissing action=eMissing_Default)

CBioseq_set_Handle	GetBioseq_setHandle (const CBioseq_set &seqset, EMissing action=eMissing_Default)

CSeq_entry_Handle	GetSeq_entryHandle (const CSeq_entry &entry, EMissing action=eMissing_Default)

CSeq_annot_Handle	GetSeq_annotHandle (const CSeq_annot &annot, EMissing action=eMissing_Default)

CSeq_feat_Handle	GetSeq_featHandle (const CSeq_feat &feat, EMissing action=eMissing_Default)

CBioseq_Handle	GetObjectHandle (const CBioseq &bioseq, EMissing action=eMissing_Default)

CBioseq_set_Handle	GetObjectHandle (const CBioseq_set &seqset, EMissing action=eMissing_Default)

CSeq_entry_Handle	GetObjectHandle (const CSeq_entry &entry, EMissing action=eMissing_Default)

CSeq_annot_Handle	GetObjectHandle (const CSeq_annot &annot, EMissing action=eMissing_Default)

CSeq_feat_Handle	GetObjectHandle (const CSeq_feat &feat, EMissing action=eMissing_Default)

CBioseq_EditHandle	GetBioseqEditHandle (const CBioseq &bioseq)
	Get edit handle for the specified object Throw an exception if object is not found, or non-editable. More...

CSeq_entry_EditHandle	GetSeq_entryEditHandle (const CSeq_entry &entry)

CSeq_annot_EditHandle	GetSeq_annotEditHandle (const CSeq_annot &annot)

CBioseq_set_EditHandle	GetBioseq_setEditHandle (const CBioseq_set &seqset)

CBioseq_EditHandle	GetObjectEditHandle (const CBioseq &bioseq)

CBioseq_set_EditHandle	GetObjectEditHandle (const CBioseq_set &seqset)

CSeq_entry_EditHandle	GetObjectEditHandle (const CSeq_entry &entry)

CSeq_annot_EditHandle	GetObjectEditHandle (const CSeq_annot &annot)

CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id &id, const CTSE_Handle &tse)
	Get bioseq handle for sequence withing one TSE. More...

CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CTSE_Handle &tse)

CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id &id, const CBioseq_Handle &bh)

CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id &id, const CSeq_entry_Handle &seh)
	Get bioseq handle for sequence withing one TSE. More...

CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CBioseq_Handle &bh)
	Get bioseq handle for sequence withing one TSE. More...

CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CSeq_entry_Handle &seh)
	Get bioseq handle for sequence withing one TSE. More...

void	AddDefaults (TPriority pri=kPriority_Default)
	Add default data loaders from object manager. More...

void	AddDataLoader (const string &loader_name, TPriority pri=kPriority_Default)
	Add data loader by name. More...

void	AddScope (CScope &scope, TPriority pri=kPriority_Default)
	Add the scope's datasources as a single group with the given priority All data sources (data loaders and explicitly added data) have priorities. More...

CSeq_entry_Handle	AddTopLevelSeqEntry (CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)
	Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with possibility to edit it directly. More...

CSeq_entry_Handle	AddTopLevelSeqEntry (const CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
	Add shared Seq-entry, scope will not modify it. More...

CBioseq_Handle	AddBioseq (CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
	Add bioseq, return bioseq handle. More...

CBioseq_Handle	AddBioseq (const CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
	Add shared Bioseq, scope will not modify it. More...

CSeq_entry_Handle	AddGC_Assembly (const CGC_Assembly &gc_assembly, CGC_Assembly_Parser::FParserFlags flags=CGC_Assembly_Parser::fDefault, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
	Add GC-Assembly. More...

CSeq_annot_Handle	AddSeq_annot (CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
	Add Seq-annot, return its CSeq_annot_Handle. More...

CSeq_annot_Handle	AddSeq_annot (const CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
	Add shared Seq-annot, scope will not modify it. More...

CSeq_entry_Handle	AddSeq_submit (CSeq_submit &submit, TPriority pri=kPriority_Default)
	Add Seq-submit, return its CSeq_entry_Handle. More...

CBioseq_EditHandle	GetEditHandle (const CBioseq_Handle &seq)
	Get editable Biosec handle by regular one. More...

CSeq_entry_EditHandle	GetEditHandle (const CSeq_entry_Handle &entry)
	Get editable SeqEntry handle by regular one. More...

CSeq_annot_EditHandle	GetEditHandle (const CSeq_annot_Handle &annot)
	Get editable Seq-annot handle by regular one. More...

CBioseq_set_EditHandle	GetEditHandle (const CBioseq_set_Handle &seqset)
	Get editable Biosec-set handle by regular one. More...

void	ResetHistory (EActionIfLocked action=eKeepIfLocked)
	Clean all unused TSEs from the scope's cache and release the memory. More...

void	ResetDataAndHistory (void)
	Clear all information in the scope except added data loaders. More...

void	ResetDataAndHistory (ERemoveDataLoaders remove_data_loaders)

void	RemoveFromHistory (const CTSE_Handle &tse, EActionIfLocked action=eKeepIfLocked)
	Remove single TSE from the scope's history. More...

void	RemoveFromHistory (const CBioseq_Handle &bioseq, EActionIfLocked action=eKeepIfLocked)
	Remove the bioseq's TSE from the scope's history. More...

void	RemoveFromHistory (const CSeq_id_Handle &seq_id)
	Remove the Seq-id failed resolution from the scope's history. More...

void	RemoveFromHistory (const CSeq_id &seq_id)
	Remove the Seq-id failed resolution from the scope's history. More...

void	RemoveDataLoader (const string &loader_name, EActionIfLocked action=eThrowIfLocked)
	Revoke data loader from the scope. More...

void	RemoveTopLevelSeqEntry (const CTSE_Handle &entry)
	Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq(). More...

void	RemoveTopLevelSeqEntry (const CSeq_entry_Handle &entry)

void	RemoveBioseq (const CBioseq_Handle &seq)
	Revoke Bioseq previously added using AddBioseq(). More...

void	RemoveSeq_annot (const CSeq_annot_Handle &annot)
	Revoke Seq-annot previously added using AddSeq_annot(). More...

bool	Exists (const CSeq_id &id)
	Check existence of sequence with this id. More...

bool	Exists (const CSeq_id_Handle &id)

TIds	GetIds (const CSeq_id &id, TGetFlags flags=0)
	Get "native" bioseq ids without filtering and matching. More...

TIds	GetIds (const CSeq_id_Handle &idh, TGetFlags flags=0)

CSeq_id_Handle	GetAccVer (const CSeq_id_Handle &idh, TGetFlags flags=0)
	Get accession.version Seq-id Returns null CSeq_id_Handle if the sequence is not found or if it doesn't have accession. More...

TGi	GetGi (const CSeq_id_Handle &idh, TGetFlags flags=0)
	Get GI of a sequence Returns ZERO_GI if the sequence is not found or if it doesn't have GI. More...

string	GetLabel (const CSeq_id &id, TGetFlags flags=0)
	Get short description of bioseq, usually "accession.version" Returns empty string if the sequence is not found. More...

string	GetLabel (const CSeq_id_Handle &idh, TGetFlags flags=0)

TTaxId	GetTaxId (const CSeq_id &id, TGetFlags flags=0)
	Get taxonomy id of bioseq Return -1 if sequence is not found Return 0 if sequence doesn't have taxonomy id. More...

TTaxId	GetTaxId (const CSeq_id_Handle &idh, TGetFlags flags=0)

TSeqPos	GetSequenceLength (const CSeq_id &id, TGetFlags flags=0)
	Get sequence length Return kInvalidSeqPos if sequence is not found. More...

TSeqPos	GetSequenceLength (const CSeq_id_Handle &id, TGetFlags flags=0)

CSeq_inst::TMol	GetSequenceType (const CSeq_id &id, TGetFlags flags=0)
	Get molecular type of sequence (protein/dna/rna) Return CSeq_inst::eMol_not_set if sequence is not found. More...

CSeq_inst::TMol	GetSequenceType (const CSeq_id_Handle &id, TGetFlags flags=0)

CBioseq_Handle::TBioseqStateFlags	GetSequenceState (const CSeq_id &id, TGetFlags flags=0)
	Get sequence GenBank state Return (fState_not_found\|fState_no_data) if sequence is not found. More...

CBioseq_Handle::TBioseqStateFlags	GetSequenceState (const CSeq_id_Handle &id, TGetFlags flags=0)

TSequenceHash	GetSequenceHash (const CSeq_id &id, TGetFlags flags=0)

TSequenceHash	GetSequenceHash (const CSeq_id_Handle &id, TGetFlags flags=0)

TBulkIds	GetBulkIds (const TSeq_id_Handles &idhs, TGetFlags flags=0)

void	GetBulkIds (TBulkIds *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TSeq_id_Handles	GetAccVers (const TSeq_id_Handles &idhs, TGetFlags flags=0)
	Get accession.version Seq-id Returns null CSeq_id_Handles for sequences that aren't found or don't have accession id. More...

void	GetAccVers (TSeq_id_Handles *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TGIs	GetGis (const TSeq_id_Handles &idhs, TGetFlags flags=0)

void	GetGis (TGIs *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TLabels	GetLabels (const TSeq_id_Handles &idhs, TGetFlags flags=0)

void	GetLabels (TLabels *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TTaxIds	GetTaxIds (const TSeq_id_Handles &idhs, TGetFlags flags=0)

void	GetTaxIds (TTaxIds *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TSequenceLengths	GetSequenceLengths (const TSeq_id_Handles &idhs, TGetFlags flags=0)

void	GetSequenceLengths (TSequenceLengths *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TSequenceTypes	GetSequenceTypes (const TSeq_id_Handles &idhs, TGetFlags flags=0)

void	GetSequenceTypes (TSequenceTypes *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TSequenceStates	GetSequenceStates (const TSeq_id_Handles &idhs, TGetFlags flags=0)

void	GetSequenceStates (TSequenceStates *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

TSequenceHashes	GetSequenceHashes (const TSeq_id_Handles &idhs, TGetFlags flags=0)

void	GetSequenceHashes (TSequenceHashes *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)

CConstRef< CSynonymsSet >	GetSynonyms (const CSeq_id &id)
	Get bioseq synonyms, resolving to the bioseq in this scope. More...

CConstRef< CSynonymsSet >	GetSynonyms (const CSeq_id_Handle &id)
	Get bioseq synonyms, resolving to the bioseq in this scope. More...

CConstRef< CSynonymsSet >	GetSynonyms (const CBioseq_Handle &bh)
	Get bioseq synonyms, resolving to the bioseq in this scope. More...

void	AttachEntry (CSeq_entry &parent, CSeq_entry &entry)

void	RemoveEntry (CSeq_entry &entry)

void	AttachAnnot (CSeq_entry &parent, CSeq_annot &annot)

void	RemoveAnnot (CSeq_entry &parent, CSeq_annot &annot)

void	ReplaceAnnot (CSeq_entry &entry, CSeq_annot &old_annot, CSeq_annot &new_annot)

CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id &id, const CSeq_entry &tse)

CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CSeq_entry &tse)

void	GetAllTSEs (TTSE_Handles &tses, enum ETSEKind kind=eManualTSEs)

CScopeTransaction	GetTransaction ()

void	UpdateAnnotIndex (void)

bool	GetKeepExternalAnnotsForEdit () const
	Return this scope's KeepExternalAnnotsForEdit flag. More...

void	SetKeepExternalAnnotsForEdit (bool keep=true)
	Change this scope's KeepExternalAnnotsForEdit flag. More...

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

Static Public Member Functions
static CSeq_id_Handle	x_GetAccVer (const TIds &ids)

static TGi	x_GetGi (const TIds &ids)

static bool	GetDefaultKeepExternalAnnotsForEdit ()
	Return current application-wide KeepExternalAnnotsForEdit flag. More...

static void	SetDefaultKeepExternalAnnotsForEdit (bool keep=true)
	Set new application-wide KeepExternalAnnotsForEdit flag. More...

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)

Protected Member Functions
CScope_Impl &	GetImpl (void)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Member Functions
	CScope (const CScope &)

CScope &	operator= (const CScope &)

Private Attributes
CRef< CScope >	m_HeapScope

CRef< CScope_Impl >	m_Impl

Friends
class	CSeqMap_CI

class	CSeq_annot_CI

class	CAnnot_Collector

class	CBioseq_CI

class	CHeapScope

class	CPrefetchTokenOld_Impl

class	CScopeTransaction

Additional Inherited Members
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...

Detailed Description

CScope –.

Scope of cache visibility and reference resolution

Definition at line 91 of file scope.hpp.

The documentation for this class was generated from the following files:

include/objmgr/scope.hpp
src/objmgr/scope.cpp
src/objmgr/scope_impl.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description