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CGather_Iter Class Reference

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#include <objtools/format/gather_iter.hpp>

+ Inheritance diagram for CGather_Iter:
+ Collaboration diagram for CGather_Iter:

Public Member Functions

 CGather_Iter (const CSeq_entry_Handle &top_seq_entry, const CFlatFileConfig &config)
 
 operator bool (void) const
 
CGather_Iteroperator++ (void)
 
const CBioseq_Handleoperator* (void) const
 
- 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 Member Functions

bool x_AddSeqEntryToStack (const CSeq_entry_Handle &seq_entry)
 
bool x_IsBioseqHandleOkay (const CBioseq_Handle &bioseq)
 

Private Attributes

std::vector< CSeq_entry_CIm_SeqEntryIterStack
 
unique_ptr< CBioseq_CIm_BioseqIter
 
const CFlatFileConfigm_Config
 
bool x_found
 

Additional Inherited Members

- 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...
 
- 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 52 of file gather_iter.hpp.

Constructor & Destructor Documentation

◆ CGather_Iter()

CGather_Iter::CGather_Iter ( const CSeq_entry_Handle top_seq_entry,
const CFlatFileConfig config 
)

Definition at line 47 of file gather_iter.cpp.

Member Function Documentation

◆ operator bool()

CGather_Iter::operator bool ( void  ) const

Definition at line 56 of file gather_iter.cpp.

◆ operator*()

const CBioseq_Handle & CGather_Iter::operator* ( void  ) const

Definition at line 96 of file gather_iter.cpp.

References _ASSERT, and m_BioseqIter.

◆ operator++()

CGather_Iter & CGather_Iter::operator++ ( void  )

◆ x_AddSeqEntryToStack()

bool CGather_Iter::x_AddSeqEntryToStack ( const CSeq_entry_Handle seq_entry)
private

◆ x_IsBioseqHandleOkay()

bool CGather_Iter::x_IsBioseqHandleOkay ( const CBioseq_Handle bioseq)
private

Definition at line 159 of file gather_iter.cpp.

References eGetId_Best, GetId(), m_Config, and CFlatFileConfig::SuppressLocalId().

Referenced by operator++(), and x_AddSeqEntryToStack().

Member Data Documentation

◆ m_BioseqIter

unique_ptr<CBioseq_CI> CGather_Iter::m_BioseqIter
private

Definition at line 78 of file gather_iter.hpp.

Referenced by operator*(), operator++(), and x_AddSeqEntryToStack().

◆ m_Config

const CFlatFileConfig& CGather_Iter::m_Config
private

Definition at line 80 of file gather_iter.hpp.

Referenced by x_AddSeqEntryToStack(), and x_IsBioseqHandleOkay().

◆ m_SeqEntryIterStack

std::vector< CSeq_entry_CI > CGather_Iter::m_SeqEntryIterStack
private

Definition at line 77 of file gather_iter.hpp.

Referenced by operator++(), and x_AddSeqEntryToStack().

◆ x_found

bool CGather_Iter::x_found
private

Definition at line 92 of file gather_iter.hpp.

Referenced by x_AddSeqEntryToStack().


The documentation for this class was generated from the following files:
Modified on Tue Apr 23 07:40:32 2024 by modify_doxy.py rev. 669887