NCBI C++ ToolKit
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CSequenceItem Class Reference

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#include <objtools/format/items/sequence_item.hpp>

+ Inheritance diagram for CSequenceItem:
+ Collaboration diagram for CSequenceItem:

Public Member Functions

 CSequenceItem (TSeqPos from, TSeqPos to, bool first, CBioseqContext &ctx)
 
void Format (IFormatter &formatter, IFlatTextOStream &text_os) const override
 
const CSeqVectorGetSequence (void) const
 
TSeqPos GetFrom (void) const
 
TSeqPos GetTo (void) const
 
bool IsFirst (void) const
 
EItem GetItemType () const override
 
- Public Member Functions inherited from CFlatItem
bool IsSetObject (void) const
 
const CSerialObjectGetObject (void) const
 
CBioseqContextGetContext (void)
 
CBioseqContextGetContext (void) const
 
bool Skip (void) const
 
bool IsExternal (void) const
 
 ~CFlatItem (void)
 
- Public Member Functions inherited from IFlatItem
virtual ~IFlatItem (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 Member Functions

void x_GatherInfo (CBioseqContext &ctx) override
 

Private Attributes

TSeqPos m_From
 
TSeqPos m_To
 
bool m_First
 
CSeqVector m_Sequence
 

Additional Inherited Members

- Public Types inherited from IFlatItem
enum  EItem {
  eItem_None = 0 , eItem_StartSection , eItem_StartItem , eItem_HtmlAnchor ,
  eItem_Head , eItem_Locus , eItem_Date , eItem_Defline ,
  eItem_Accession , eItem_Version , eItem_Project , eItem_GenomeProject ,
  eItem_DbSource , eItem_Keywords , eItem_Segment , eItem_Source ,
  eItem_Reference , eItem_Cache , eItem_Comment , eItem_Primary ,
  eItem_FeatHeader , eItem_SourceFeat , eItem_Feature , eItem_Gap ,
  eItem_BaseCount , eItem_Origin , eItem_Sequence , eItem_Contig ,
  eItem_Wgs , eItem_Tsa , eItem_Alignment , eItem_EndItem ,
  eItem_EndSection , eItem_Slash
}
 
- 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 CFlatItem
 CFlatItem (CBioseqContext *ctx=0)
 
void x_SetObject (const CSerialObject &obj)
 
void x_SetContext (CBioseqContext &ctx)
 
void x_SetSkip (void)
 
void x_SetExternal (void)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 55 of file sequence_item.hpp.

Constructor & Destructor Documentation

◆ CSequenceItem()

CSequenceItem::CSequenceItem ( TSeqPos  from,
TSeqPos  to,
bool  first,
CBioseqContext ctx 
)

Definition at line 50 of file sequence_item.cpp.

References ctx.

Member Function Documentation

◆ Format()

void CSequenceItem::Format ( IFormatter formatter,
IFlatTextOStream text_os 
) const
overridevirtual

Implements CFlatItem.

Definition at line 67 of file sequence_item.cpp.

References IFormatter::FormatSequence().

◆ GetFrom()

TSeqPos CSequenceItem::GetFrom ( void  ) const
inline

◆ GetItemType()

IFlatItem::EItem CSequenceItem::GetItemType ( void  ) const
overridevirtual

Implements IFlatItem.

Definition at line 62 of file sequence_item.cpp.

References IFlatItem::eItem_Sequence.

◆ GetSequence()

const CSeqVector & CSequenceItem::GetSequence ( void  ) const
inline

◆ GetTo()

TSeqPos CSequenceItem::GetTo ( void  ) const
inline

◆ IsFirst()

bool CSequenceItem::IsFirst ( void  ) const
inline

Definition at line 101 of file sequence_item.hpp.

References m_First.

Referenced by CGBSeqFormatter::FormatSequence(), and CGenbankFormatter::FormatSequence().

◆ x_GatherInfo()

void CSequenceItem::x_GatherInfo ( CBioseqContext ctx)
overrideprivatevirtual

Member Data Documentation

◆ m_First

bool CSequenceItem::m_First
private

Definition at line 73 of file sequence_item.hpp.

Referenced by IsFirst().

◆ m_From

TSeqPos CSequenceItem::m_From
private

Definition at line 72 of file sequence_item.hpp.

Referenced by GetFrom().

◆ m_Sequence

CSeqVector CSequenceItem::m_Sequence
private

Definition at line 74 of file sequence_item.hpp.

Referenced by GetSequence(), and x_GatherInfo().

◆ m_To

TSeqPos CSequenceItem::m_To
private

Definition at line 72 of file sequence_item.hpp.

Referenced by GetTo().


The documentation for this class was generated from the following files:
Modified on Sat Dec 02 09:22:27 2023 by modify_doxy.py rev. 669887