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CFlatItem Class Referenceabstract

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

+ Inheritance diagram for CFlatItem:
+ Collaboration diagram for CFlatItem:

Public Member Functions

virtual void Format (IFormatter &formatter, IFlatTextOStream &text_os) const =0
 
bool IsSetObject (void) const
 
const CSerialObject * GetObject (void) const
 
CBioseqContext * GetContext (void)
 
CBioseqContext * GetContext (void) const
 
bool Skip (void) const
 
bool IsExternal (void) const
 
 ~CFlatItem (void)
 
- Public Member Functions inherited from IFlatItem
virtual EItem GetItemType (void) const =0
 
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...
 
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

 CFlatItem (CBioseqContext *ctx=0)
 
virtual void x_GatherInfo (CBioseqContext &)
 
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...
 

Private Attributes

CConstRef< CSerialObject > m_Object
 
CBioseqContext * m_Context
 
bool m_Skip
 
bool m_External
 

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< Uint8 > TCounter
 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...
 

Detailed Description

Definition at line 49 of file item_base.hpp.

Constructor & Destructor Documentation

◆ ~CFlatItem()

CFlatItem::~CFlatItem ( void  )
inline

Definition at line 141 of file item_base.hpp.

◆ CFlatItem()

CFlatItem::CFlatItem ( CBioseqContext *  ctx = 0)
inlineprotected

Definition at line 149 of file item_base.hpp.

Member Function Documentation

◆ Format()

virtual void CFlatItem::Format ( IFormatter &  formatter,
IFlatTextOStream &  text_os 
) const
pure virtual

Implements IFlatItem.

Implemented in CWGSItem, CVersionItem, CTSAItem, CSourceItem, CSequenceItem, CSegmentItem, CReferenceItem, CCacheItem, CPrimaryItem, COriginItem, CLocusItem, CKeywordsItem, CHtmlAnchorItem, CGenomeProjectItem, CGapItem, CFeatHeaderItem, CDeflineItem, CDBSourceItem, CDateItem, CContigItem, CCommentItem, CBaseCountItem, CAlignmentItem, CAccessionItem, CGenomeItem, CFeatureItemBase, CEndItem, CEndSectionItem, CStartSectionItem, and CStartItem.

◆ GetContext() [1/2]

CBioseqContext * CFlatItem::GetContext ( void  )
inline

Definition at line 113 of file item_base.hpp.

References m_Context.

Referenced by CFlatFileFactoryBuilder::AddItem(), CFlatFileSequenceListJob::CFlatFileSeqBuilder::AddItem(), CFlatFileTextItem::CFlatFileTextItem(), CGenbankFormatter::EndSection(), CFeatureItemBase::Format(), CGBSeqFormatter::FormatAccession(), CGenbankFormatter::FormatAccession(), CGBSeqFormatter::FormatContig(), CGenbankFormatter::FormatContig(), CGenbankFormatter::FormatDBSource(), CGBSeqFormatter::FormatGap(), CGenbankFormatter::FormatGenomeProject(), CGenbankFormatter::FormatHtmlAnchor(), CGenbankFormatter::FormatKeywords(), CEmblFormatter::FormatLocus(), CGBSeqFormatter::FormatLocus(), CGenbankFormatter::FormatLocus(), CGenbankFormatter::FormatPrimary(), CGBSeqFormatter::FormatReference(), CGenbankFormatter::FormatReference(), CGenbankFormatter::FormatSequence(), CGenbankFormatter::FormatTSA(), CGenbankFormatter::FormatWGS(), CFlatFileLocusItem::GetBioseqHandle(), CFlatFileViewContext::GetEditObject(), CFeatureItem::GetKey(), CBioseqEditor::IsEditable(), CFlatFileLocusItem::OnHyperlinkClick(), s_CombineRefs(), s_FormatRegularSequencePiece(), s_GetContext(), s_GetLinkFeatureKey(), CReferenceItem::SetRemark(), CSUCTextGather::unified_notify(), CFeatureItem::x_AddFTableCdregionQuals(), CFeatureItem::x_AddFTableExtQuals(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualProteinId(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsGene(), CGenbankFormatter::x_Authors(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CFeatureItem::x_CleanQuals(), CGenbankFormatter::x_Consortium(), CFlatItemFormatter::x_FormatAccession(), CDBSourceItem::x_FormatDBSourceID(), CSourceFeatureItem::x_FormatGBNoteQuals(), CFeatureItem::x_FormatGOQualCombined(), CFeatureItem::x_FormatNoteQual(), CFeatureItem::x_FormatNoteQuals(), CSourceFeatureItem::x_FormatNoteQuals(), CDBSourceItem::x_FormatPDBSource(), CFeatureItem::x_FormatQual(), CSourceFeatureItem::x_FormatQual(), CFeatureItem::x_FormatQuals(), CSourceFeatureItem::x_FormatQuals(), CCommentItem::x_GatherDescInfo(), CCommentItem::x_GatherUserObjInfo(), CGenbankFormatter::x_Journal(), CGenbankFormatter::x_Reference(), CGenbankFormatter::x_SmartWrapQuals(), and CGenbankFormatter::x_Title().

◆ GetContext() [2/2]

CBioseqContext * CFlatItem::GetContext ( void  ) const
inline

Definition at line 120 of file item_base.hpp.

References m_Context.

◆ GetObject()

const CSerialObject * CFlatItem::GetObject ( void  ) const
inlinevirtual

Implements IFlatItem.

Definition at line 99 of file item_base.hpp.

References m_Object.

Referenced by CGBSeqFormatter::FormatAccession(), CGenbankFormatter::FormatAccession(), CGenbankFormatter::FormatBasecount(), CGenbankFormatter::FormatComment(), CGBSeqFormatter::FormatContig(), CGenbankFormatter::FormatContig(), CGenbankFormatter::FormatDBSource(), CGBSeqFormatter::FormatDefline(), CGenbankFormatter::FormatDefline(), CGBSeqFormatter::FormatGap(), CGenbankFormatter::FormatGap(), CGBSeqFormatter::FormatGenomeProject(), CGenbankFormatter::FormatGenomeProject(), CGBSeqFormatter::FormatKeywords(), CGenbankFormatter::FormatKeywords(), CGBSeqFormatter::FormatLocus(), CGenbankFormatter::FormatLocus(), CGenbankFormatter::FormatPrimary(), CGBSeqFormatter::FormatReference(), CGenbankFormatter::FormatReference(), CGBSeqFormatter::FormatSegment(), CGenbankFormatter::FormatSegment(), CGBSeqFormatter::FormatSequence(), CGenbankFormatter::FormatTSA(), CGenbankFormatter::FormatWGS(), CFlatFileViewContext::GetEditObject(), s_FormatRegularSequencePiece(), CCommentItem::x_GatherInfo(), CLocusItem::x_SetBiomol(), and CLocusItem::x_SetDivision().

◆ IsExternal()

bool CFlatItem::IsExternal ( void  ) const
inline

Definition at line 134 of file item_base.hpp.

References m_External.

◆ IsSetObject()

bool CFlatItem::IsSetObject ( void  ) const
inline

Definition at line 106 of file item_base.hpp.

References m_Object, and CConstRef< C, Locker >::NotEmpty().

Referenced by CKeywordsItem::x_GatherInfo().

◆ Skip()

bool CFlatItem::Skip ( void  ) const
inlinevirtual

Implements IFlatItem.

Definition at line 127 of file item_base.hpp.

References m_Skip.

Referenced by CEmblFormatter::FormatCache(), CGBSeqFormatter::FormatCache(), CGenbankFormatter::FormatCache(), CEmblFormatter::FormatDefline(), and CEmblFormatter::FormatKeywords().

◆ x_GatherInfo()

virtual void CFlatItem::x_GatherInfo ( CBioseqContext &  )
inlineprotectedvirtual

Reimplemented in CWGSItem, CVersionItem, CTSAItem, CSourceItem, CSequenceItem, CSegmentItem, CReferenceItem, CPrimaryItem, COriginItem, CLocusItem, CKeywordsItem, CHtmlAnchorItem, CGenomeProjectItem, CSourceFeatureItem, CFeatHeaderItem, CDeflineItem, CDBSourceItem, CDateItem, CContigItem, CCommentItem, CBaseCountItem, CAlignmentItem, CAccessionItem, CGenomeItem, CFileIdComment, CLocalIdComment, CGsdbComment, CHistComment, CGenomeAnnotComment, and CGapItem.

Definition at line 71 of file item_base.hpp.

◆ x_SetContext()

void CFlatItem::x_SetContext ( CBioseqContext &  ctx)
protected

◆ x_SetExternal()

void CFlatItem::x_SetExternal ( void  )
inlineprotected

Definition at line 176 of file item_base.hpp.

References m_External.

Referenced by CFeatureItemBase::CFeatureItemBase().

◆ x_SetObject()

void CFlatItem::x_SetObject ( const CSerialObject &  obj)
inlineprotected

Definition at line 160 of file item_base.hpp.

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

Referenced by CCommentItem::CCommentItem(), CFeatureItemBase::CFeatureItemBase(), CReferenceItem::CReferenceItem(), CSourceFeatureItem::CSourceFeatureItem(), CSourceFeatureItem::SetObject(), CDBSourceItem::x_AddPDBBlock(), CDBSourceItem::x_AddPIRBlock(), CDBSourceItem::x_AddPRFBlock(), CDBSourceItem::x_AddSPBlock(), CAccessionItem::x_GatherInfo(), CDeflineItem::x_GatherInfo(), CGenomeProjectItem::x_GatherInfo(), CKeywordsItem::x_GatherInfo(), CLocusItem::x_GatherInfo(), COriginItem::x_GatherInfo(), CPrimaryItem::x_GatherInfo(), CSequenceItem::x_GatherInfo(), and CSourceItem::x_SetSource().

◆ x_SetSkip()

void CFlatItem::x_SetSkip ( void  )
inlineprotected

Definition at line 167 of file item_base.hpp.

References m_Context, m_Object, m_Skip, and CConstRef< C, Locker >::Reset().

Referenced by CReferenceItem::CReferenceItem(), CSourceFeatureItem::CSourceFeatureItem(), CAccessionItem::x_GatherInfo(), CBaseCountItem::x_GatherInfo(), CSourceFeatureItem::x_GatherInfo(), CHtmlAnchorItem::x_GatherInfo(), CFeatureItem::x_GatherInfoWithParent(), CReferenceItem::x_Init(), and CCommentItem::x_SetSkip().

Member Data Documentation

◆ m_Context

CBioseqContext* CFlatItem::m_Context
private

Definition at line 84 of file item_base.hpp.

Referenced by GetContext(), and x_SetSkip().

◆ m_External

bool CFlatItem::m_External
private

Definition at line 88 of file item_base.hpp.

Referenced by IsExternal(), and x_SetExternal().

◆ m_Object

CConstRef<CSerialObject> CFlatItem::m_Object
private

Definition at line 82 of file item_base.hpp.

Referenced by GetObject(), IsSetObject(), x_SetObject(), and x_SetSkip().

◆ m_Skip

bool CFlatItem::m_Skip
private

Definition at line 86 of file item_base.hpp.

Referenced by Skip(), and x_SetSkip().

The documentation for this class was generated from the following file:
Generated by doxygen 1.9.0
Modified on Tue Apr 30 06:40:52 2024 by modify_doxy.py rev. 669887