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CFlatFileContext Class Reference

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#include <objtools/format/context.hpp>

+ Inheritance diagram for CFlatFileContext:
+ Collaboration diagram for CFlatFileContext:

Public Types

typedef CRef< CBioseqContextTSection
 
typedef vector< CRef< CBioseqContext > > TSections
 
- 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CFlatFileContext (const CFlatFileConfig &cfg)
 
 ~CFlatFileContext (void)
 
const CSeq_entry_HandleGetEntry (void) const
 
void SetEntry (const CSeq_entry_Handle &entry)
 
const CSubmit_blockGetSubmitBlock (void) const
 
void SetSubmit (const CSubmit_block &sub)
 
const CFlatFileConfigGetConfig (void) const
 
CFlatFileConfigSetConfig (void)
 
void SetConfig (const CFlatFileConfig &cfg)
 
const SAnnotSelectorGetAnnotSelector (void) const
 
SAnnotSelectorSetAnnotSelector (void)
 
void SetAnnotSelector (const SAnnotSelector &)
 
const CSeq_locGetLocation (void) const
 
void SetLocation (const CSeq_loc *loc)
 
const feature::CFeatTree * GetFeatTree (void) const
 
feature::CFeatTree * GetFeatTree (void)
 
void SetFeatTree (feature::CFeatTree *tree)
 
bool UsingSeqEntryIndex (void) const
 
const CRef< CSeqEntryIndexGetSeqEntryIndex (void) const
 
void SetSeqEntryIndex (CRef< CSeqEntryIndex > idx)
 
void ResetSeqEntryIndex (void)
 
bool GetSGS (void) const
 
void SetSGS (const bool sgs)
 
void AddSection (TSection &section)
 
void Reset (void)
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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
 

Private Attributes

CFlatFileConfig m_Cfg
 
CSeq_entry_Handle m_Entry
 
TSections m_Sections
 
CConstRef< CSubmit_blockm_Submit
 
unique_ptr< SAnnotSelectorm_Selector
 
CConstRef< CSeq_locm_Loc
 
CRef< feature::CFeatTree > m_FeatTree
 
CRef< CSeqEntryIndexm_Idx
 
bool m_SmallGenomeSet
 

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

Detailed Description

Definition at line 437 of file context.hpp.

Member Typedef Documentation

◆ TSection

Definition at line 441 of file context.hpp.

◆ TSections

Definition at line 442 of file context.hpp.

Constructor & Destructor Documentation

◆ CFlatFileContext()

CFlatFileContext::CFlatFileContext ( const CFlatFileConfig cfg)
inline

Definition at line 445 of file context.hpp.

◆ ~CFlatFileContext()

CFlatFileContext::~CFlatFileContext ( void  )
inline

Definition at line 447 of file context.hpp.

Member Function Documentation

◆ AddSection()

void CFlatFileContext::AddSection ( TSection section)
inline

Definition at line 478 of file context.hpp.

References m_Sections.

Referenced by CFlatGatherer::x_DoMultipleSections(), and CFlatGatherer::x_GatherBioseq().

◆ GetAnnotSelector()

const SAnnotSelector * CFlatFileContext::GetAnnotSelector ( void  ) const
inline

Definition at line 763 of file context.hpp.

References m_Selector.

Referenced by CBioseqContext::GetAnnotSelector().

◆ GetConfig()

const CFlatFileConfig& CFlatFileContext::GetConfig ( void  ) const
inline

◆ GetEntry()

const CSeq_entry_Handle& CFlatFileContext::GetEntry ( void  ) const
inline

Definition at line 449 of file context.hpp.

References m_Entry.

Referenced by CBioseqContext::GetTopLevelEntry().

◆ GetFeatTree() [1/2]

feature::CFeatTree* CFlatFileContext::GetFeatTree ( void  )
inline

Definition at line 467 of file context.hpp.

References m_FeatTree.

◆ GetFeatTree() [2/2]

const feature::CFeatTree* CFlatFileContext::GetFeatTree ( void  ) const
inline

Definition at line 466 of file context.hpp.

References m_FeatTree.

◆ GetLocation()

const CSeq_loc* CFlatFileContext::GetLocation ( void  ) const
inline

◆ GetSeqEntryIndex()

const CRef<CSeqEntryIndex> CFlatFileContext::GetSeqEntryIndex ( void  ) const
inline

◆ GetSGS()

bool CFlatFileContext::GetSGS ( void  ) const
inline

Definition at line 475 of file context.hpp.

References m_SmallGenomeSet.

Referenced by CBioseqContext::GetSGS().

◆ GetSubmitBlock()

const CSubmit_block* CFlatFileContext::GetSubmitBlock ( void  ) const
inline

Definition at line 452 of file context.hpp.

References m_Submit.

Referenced by CBioseqContext::GetSubmitBlock().

◆ Reset()

void CFlatFileContext::Reset ( void  )
inline

◆ ResetSeqEntryIndex()

void CFlatFileContext::ResetSeqEntryIndex ( void  )
inline

◆ SetAnnotSelector() [1/2]

void CFlatFileContext::SetAnnotSelector ( const SAnnotSelector sel)
inline

Definition at line 780 of file context.hpp.

References m_Selector.

◆ SetAnnotSelector() [2/2]

SAnnotSelector & CFlatFileContext::SetAnnotSelector ( void  )
inline

◆ SetConfig() [1/2]

void CFlatFileContext::SetConfig ( const CFlatFileConfig cfg)
inline

Definition at line 457 of file context.hpp.

References m_Cfg.

◆ SetConfig() [2/2]

CFlatFileConfig& CFlatFileContext::SetConfig ( void  )
inline

◆ SetEntry()

void CFlatFileContext::SetEntry ( const CSeq_entry_Handle entry)
inline

Definition at line 450 of file context.hpp.

References m_Entry.

Referenced by CFlatFileGenerator::Generate().

◆ SetFeatTree()

void CFlatFileContext::SetFeatTree ( feature::CFeatTree *  tree)
inline

Definition at line 468 of file context.hpp.

References m_FeatTree, and CRef< C, Locker >::Reset().

Referenced by CFlatFileGenerator::SetFeatTree().

◆ SetLocation()

void CFlatFileContext::SetLocation ( const CSeq_loc loc)
inline

Definition at line 464 of file context.hpp.

References m_Loc, and CConstRef< C, Locker >::Reset().

Referenced by CFlatFileGenerator::Generate().

◆ SetSeqEntryIndex()

void CFlatFileContext::SetSeqEntryIndex ( CRef< CSeqEntryIndex idx)
inline

Definition at line 472 of file context.hpp.

References m_Idx.

Referenced by CFlatFileGenerator::Generate(), and CFlatFileGenerator::SetSeqEntryIndex().

◆ SetSGS()

void CFlatFileContext::SetSGS ( const bool  sgs)
inline

Definition at line 476 of file context.hpp.

References m_SmallGenomeSet.

Referenced by CFlatFileGenerator::Generate().

◆ SetSubmit()

void CFlatFileContext::SetSubmit ( const CSubmit_block sub)
inline

Definition at line 453 of file context.hpp.

References m_Submit.

Referenced by CFlatFileGenerator::Generate(), and CFlatFileGenerator::SetSubmit().

◆ UsingSeqEntryIndex()

bool CFlatFileContext::UsingSeqEntryIndex ( void  ) const
inline

Member Data Documentation

◆ m_Cfg

CFlatFileConfig CFlatFileContext::m_Cfg
private

Definition at line 484 of file context.hpp.

Referenced by GetConfig(), and SetConfig().

◆ m_Entry

CSeq_entry_Handle CFlatFileContext::m_Entry
private

Definition at line 485 of file context.hpp.

Referenced by GetEntry(), Reset(), and SetEntry().

◆ m_FeatTree

CRef<feature::CFeatTree> CFlatFileContext::m_FeatTree
private

Definition at line 490 of file context.hpp.

Referenced by GetFeatTree(), and SetFeatTree().

◆ m_Idx

CRef<CSeqEntryIndex> CFlatFileContext::m_Idx
private

◆ m_Loc

CConstRef<CSeq_loc> CFlatFileContext::m_Loc
private

Definition at line 489 of file context.hpp.

Referenced by GetLocation(), Reset(), and SetLocation().

◆ m_Sections

TSections CFlatFileContext::m_Sections
private

Definition at line 486 of file context.hpp.

Referenced by AddSection(), and Reset().

◆ m_Selector

unique_ptr<SAnnotSelector> CFlatFileContext::m_Selector
private

Definition at line 488 of file context.hpp.

Referenced by GetAnnotSelector(), Reset(), and SetAnnotSelector().

◆ m_SmallGenomeSet

bool CFlatFileContext::m_SmallGenomeSet
private

Definition at line 492 of file context.hpp.

Referenced by GetSGS(), Reset(), and SetSGS().

◆ m_Submit

CConstRef<CSubmit_block> CFlatFileContext::m_Submit
private

Definition at line 487 of file context.hpp.

Referenced by GetSubmitBlock(), Reset(), and SetSubmit().


The documentation for this class was generated from the following file:
Modified on Sat Dec 02 09:20:15 2023 by modify_doxy.py rev. 669887