NCBI C++ ToolKit
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CFeatureItemBase Class Referenceabstract

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

+ Inheritance diagram for CFeatureItemBase:
+ Collaboration diagram for CFeatureItemBase:

Public Member Functions

CConstRef< CFlatFeatureFormat (void) const
 
void Format (IFormatter &formatter, IFlatTextOStream &text_os) const
 
bool operator< (const CFeatureItemBase &f2) const
 
const CMappedFeatGetFeat (void) const
 
const CSeq_locGetLoc (void) const
 
virtual string GetKey (void) const
 
bool IsSuppressAccession (void) const
 
- 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 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...
 
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
 

Protected Member Functions

 CFeatureItemBase (const CMappedFeat &feat, CBioseqContext &ctx, CRef< feature::CFeatTree > ftree, const CSeq_loc *loc=0, bool suppressAccession=false)
 
virtual void x_AddQuals (CBioseqContext &ctx)=0
 
virtual void x_FormatQuals (CFlatFeature &ff) const =0
 
- Protected Member Functions inherited from CFlatItem
 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...
 

Protected Attributes

CMappedFeat m_Feat
 
CRef< feature::CFeatTree > m_Feat_Tree
 
CConstRef< CSeq_locm_Loc
 
bool m_SuppressAccession
 

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...
 

Detailed Description

Definition at line 109 of file feature_item.hpp.

Constructor & Destructor Documentation

◆ CFeatureItemBase()

CFeatureItemBase::CFeatureItemBase ( const CMappedFeat feat,
CBioseqContext ctx,
CRef< feature::CFeatTree >  ftree,
const CSeq_loc loc = 0,
bool  suppressAccession = false 
)
protected

Member Function Documentation

◆ Format() [1/2]

void CFeatureItemBase::Format ( IFormatter formatter,
IFlatTextOStream text_os 
) const
inlinevirtual

Implements CFlatItem.

Definition at line 115 of file feature_item.hpp.

References IFormatter::FormatFeature().

◆ Format() [2/2]

CConstRef< CFlatFeature > CFeatureItemBase::Format ( void  ) const

◆ GetFeat()

const CMappedFeat& CFeatureItemBase::GetFeat ( void  ) const
inline

◆ GetKey()

virtual string CFeatureItemBase::GetKey ( void  ) const
inlinevirtual

◆ GetLoc()

const CSeq_loc& CFeatureItemBase::GetLoc ( void  ) const
inline

◆ IsSuppressAccession()

bool CFeatureItemBase::IsSuppressAccession ( void  ) const
inline

Definition at line 129 of file feature_item.hpp.

References m_SuppressAccession.

Referenced by Format().

◆ operator<()

bool CFeatureItemBase::operator< ( const CFeatureItemBase f2) const
inline

Definition at line 118 of file feature_item.hpp.

References m_Feat.

◆ x_AddQuals()

virtual void CFeatureItemBase::x_AddQuals ( CBioseqContext ctx)
protectedpure virtual

Implemented in CSourceFeatureItem, and CFeatureItem.

◆ x_FormatQuals()

virtual void CFeatureItemBase::x_FormatQuals ( CFlatFeature ff) const
protectedpure virtual

Implemented in CSourceFeatureItem, and CFeatureItem.

Referenced by Format().

Member Data Documentation

◆ m_Feat

CMappedFeat CFeatureItemBase::m_Feat
protected

Definition at line 141 of file feature_item.hpp.

Referenced by CFeatureItemBase(), CSourceFeatureItem::CSourceFeatureItem(), Format(), GetFeat(), GetKey(), CFeatureItem::GetKey(), CSourceFeatureItem::GetSource(), operator<(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualCitation(), CFeatureItem::x_AddQualCodedBy(), CFeatureItem::x_AddQualDbXref(), CFeatureItem::x_AddQualExceptions(), CFeatureItem::x_AddQualExpInv(), CFeatureItem::x_AddQualExt(), CFeatureItem::x_AddQualGeneXref(), CFeatureItem::x_AddQualOldLocusTag(), CFeatureItem::x_AddQualOperon(), CFeatureItem::x_AddQualPartial(), CFeatureItem::x_AddQualProteinConflict(), CSourceFeatureItem::x_AddQuals(), CFeatureItem::x_AddQuals(), CFeatureItem::x_AddQualsBond(), CFeatureItem::x_AddQualsCdregion(), CFeatureItem::x_AddQualsCdregionIdx(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsExt(), CFeatureItem::x_AddQualsGb(), CFeatureItem::x_AddQualsGene(), CFeatureItem::x_AddQualsHet(), CFeatureItem::x_AddQualsIdx(), CFeatureItem::x_AddQualsNonStd(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsPsecStr(), CFeatureItem::x_AddQualsRegion(), CFeatureItem::x_AddQualsRegulatoryClass(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualsSite(), CFeatureItem::x_AddQualsVariation(), CFeatureItem::x_AddQualTranslation(), CFeatureItem::x_AddRegulatoryClassQual(), CFeatureItem::x_CleanQuals(), CFeatureItem::x_DropIllegalQuals(), CSourceFeatureItem::x_GatherInfo(), CFeatureItem::x_GatherInfoWithParent(), CFeatureItem::x_GetAssociatedProtInfo(), CFeatureItem::x_GetAssociatedProtInfoIdx(), CFeatureItem::x_HasMethodtRNAscanSE(), CFeatureItem::x_ImportQuals(), and CFeatureItem::x_IsSeqFeatDataFeatureLegal().

◆ m_Feat_Tree

CRef<feature::CFeatTree> CFeatureItemBase::m_Feat_Tree
protected

Definition at line 142 of file feature_item.hpp.

Referenced by CFeatureItem::x_AddQuals().

◆ m_Loc

CConstRef<CSeq_loc> CFeatureItemBase::m_Loc
protected

◆ m_SuppressAccession

bool CFeatureItemBase::m_SuppressAccession
protected

Definition at line 144 of file feature_item.hpp.

Referenced by IsSuppressAccession().


The documentation for this class was generated from the following files:
Modified on Sun Apr 21 03:39:03 2024 by modify_doxy.py rev. 669887