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CSourceFeatureItem Class Reference

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

+ Inheritance diagram for CSourceFeatureItem:
+ Collaboration diagram for CSourceFeatureItem:

Public Types

typedef CRange< TSeqPosTRange
 
- 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...
 

Public Member Functions

 CSourceFeatureItem (const CBioSource &src, TRange range, CBioseqContext &ctx, CRef< feature::CFeatTree > ftree)
 
 CSourceFeatureItem (const CMappedFeat &feat, CBioseqContext &ctx, CRef< feature::CFeatTree > ftree, const CSeq_loc *loc=nullptr)
 
void SetObject (const CSerialObject &obj)
 
bool WasDesc (void) const
 
const CBioSourceGetSource (void) const
 
string GetKey (void) const override
 
bool IsFocus (void) const
 
bool IsSynthetic (void) const
 
void Subtract (const CSourceFeatureItem &other, CScope &scope)
 
void SetLoc (const CSeq_loc &loc)
 
EItem GetItemType () const override
 
- Public Member Functions inherited from CFeatureItemBase
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
 
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 ~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 Types

typedef CQualContainer< ESourceQualifierTQuals
 
typedef TQuals::const_iterator TQCI
 
typedef IFlatQVal::TFlags TQualFlags
 

Private Member Functions

void x_GatherInfo (CBioseqContext &ctx) override
 
void x_AddQuals (CBioseqContext &ctx) override
 
void x_AddQuals (const CBioSource &src, CBioseqContext &ctx) const
 
void x_AddQuals (const COrg_ref &org, CBioseqContext &ctx) const
 
void x_AddPcrPrimersQuals (const CBioSource &src, CBioseqContext &ctx) const
 
void x_AddQual (ESourceQualifier slot, const IFlatQVal *value) const
 
void x_FormatQuals (CFlatFeature &ff) const override
 
void x_FormatGBNoteQuals (CFlatFeature &ff) const
 
void x_FormatNoteQuals (CFlatFeature &ff) const
 
void x_FormatQual (ESourceQualifier slot, const CTempString &name, CFlatFeature::TQuals &qvec, TQualFlags flags=0) const
 
void x_FormatNoteQual (ESourceQualifier slot, const char *name, CFlatFeature::TQuals &qvec, TQualFlags flags=0) const
 

Private Attributes

bool m_WasDesc
 
TQuals m_Quals
 
bool m_IsFocus
 
bool m_IsSynthetic
 
CRef< feature::CFeatTree > m_Feat_Tree
 

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 CFeatureItemBase
 CFeatureItemBase (const CMappedFeat &feat, CBioseqContext &ctx, CRef< feature::CFeatTree > ftree, const CSeq_loc *loc=0, bool suppressAccession=false)
 
- 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...
 
- Protected Attributes inherited from CFeatureItemBase
CMappedFeat m_Feat
 
CRef< feature::CFeatTree > m_Feat_Tree
 
CConstRef< CSeq_locm_Loc
 
bool m_SuppressAccession
 

Detailed Description

Definition at line 398 of file feature_item.hpp.

Member Typedef Documentation

◆ TQCI

Definition at line 428 of file feature_item.hpp.

◆ TQualFlags

Definition at line 429 of file feature_item.hpp.

◆ TQuals

Definition at line 427 of file feature_item.hpp.

◆ TRange

Definition at line 403 of file feature_item.hpp.

Constructor & Destructor Documentation

◆ CSourceFeatureItem() [1/2]

CSourceFeatureItem::CSourceFeatureItem ( const CBioSource src,
TRange  range,
CBioseqContext ctx,
CRef< feature::CFeatTree >  ftree 
)

◆ CSourceFeatureItem() [2/2]

CSourceFeatureItem::CSourceFeatureItem ( const CMappedFeat feat,
CBioseqContext ctx,
CRef< feature::CFeatTree >  ftree,
const CSeq_loc loc = nullptr 
)

Definition at line 6093 of file feature_item.cpp.

References ctx, and x_GatherInfo().

Member Function Documentation

◆ GetItemType()

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

Implements IFlatItem.

Definition at line 6105 of file feature_item.cpp.

References IFlatItem::eItem_SourceFeat.

◆ GetKey()

string CSourceFeatureItem::GetKey ( void  ) const
inlineoverridevirtual

Reimplemented from CFeatureItemBase.

Definition at line 416 of file feature_item.hpp.

◆ GetSource()

const CBioSource& CSourceFeatureItem::GetSource ( void  ) const
inline

◆ IsFocus()

bool CSourceFeatureItem::IsFocus ( void  ) const
inline

Definition at line 418 of file feature_item.hpp.

References m_IsFocus.

Referenced by CFlatGatherer::x_BiosourcesEqualForMergingPurposes().

◆ IsSynthetic()

bool CSourceFeatureItem::IsSynthetic ( void  ) const
inline

Definition at line 419 of file feature_item.hpp.

References m_IsSynthetic.

◆ SetLoc()

void CSourceFeatureItem::SetLoc ( const CSeq_loc loc)

Definition at line 6781 of file feature_item.cpp.

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

◆ SetObject()

void CSourceFeatureItem::SetObject ( const CSerialObject obj)
inline

Definition at line 410 of file feature_item.hpp.

References CFlatItem::x_SetObject().

◆ Subtract()

void CSourceFeatureItem::Subtract ( const CSourceFeatureItem other,
CScope scope 
)

◆ WasDesc()

bool CSourceFeatureItem::WasDesc ( void  ) const
inline

Definition at line 412 of file feature_item.hpp.

References m_WasDesc.

Referenced by x_AddQuals().

◆ x_AddPcrPrimersQuals()

void CSourceFeatureItem::x_AddPcrPrimersQuals ( const CBioSource src,
CBioseqContext ctx 
) const
private

◆ x_AddQual()

void CSourceFeatureItem::x_AddQual ( ESourceQualifier  slot,
const IFlatQVal value 
) const
inlineprivate

Definition at line 439 of file feature_item.hpp.

References CQualContainer< Key >::AddQual(), m_Quals, and rapidjson::value.

Referenced by x_AddPcrPrimersQuals(), and x_AddQuals().

◆ x_AddQuals() [1/3]

void CSourceFeatureItem::x_AddQuals ( CBioseqContext ctx)
overrideprivatevirtual

◆ x_AddQuals() [2/3]

void CSourceFeatureItem::x_AddQuals ( const CBioSource src,
CBioseqContext ctx 
) const
private

◆ x_AddQuals() [3/3]

void CSourceFeatureItem::x_AddQuals ( const COrg_ref org,
CBioseqContext ctx 
) const
private

◆ x_FormatGBNoteQuals()

void CSourceFeatureItem::x_FormatGBNoteQuals ( CFlatFeature ff) const
private

Definition at line 6553 of file feature_item.cpp.

References _ASSERT, DO_QUAL, CFlatItem::GetContext(), and CFlatFeature::SetQuals().

Referenced by x_FormatQuals().

◆ x_FormatNoteQual()

void CSourceFeatureItem::x_FormatNoteQual ( ESourceQualifier  slot,
const char *  name,
CFlatFeature::TQuals qvec,
TQualFlags  flags = 0 
) const
inlineprivate

Definition at line 448 of file feature_item.hpp.

References IFlatQVal::fIsNote, flags, and x_FormatQual().

Referenced by x_FormatNoteQuals().

◆ x_FormatNoteQuals()

void CSourceFeatureItem::x_FormatNoteQuals ( CFlatFeature ff) const
private

◆ x_FormatQual()

void CSourceFeatureItem::x_FormatQual ( ESourceQualifier  slot,
const CTempString name,
CFlatFeature::TQuals qvec,
TQualFlags  flags = 0 
) const
private

◆ x_FormatQuals()

void CSourceFeatureItem::x_FormatQuals ( CFlatFeature ff) const
overrideprivatevirtual

◆ x_GatherInfo()

void CSourceFeatureItem::x_GatherInfo ( CBioseqContext ctx)
overrideprivatevirtual

Member Data Documentation

◆ m_Feat_Tree

CRef<feature::CFeatTree> CSourceFeatureItem::m_Feat_Tree
private

Definition at line 457 of file feature_item.hpp.

◆ m_IsFocus

bool CSourceFeatureItem::m_IsFocus
private

Definition at line 455 of file feature_item.hpp.

Referenced by IsFocus(), and x_GatherInfo().

◆ m_IsSynthetic

bool CSourceFeatureItem::m_IsSynthetic
private

Definition at line 456 of file feature_item.hpp.

Referenced by IsSynthetic(), and x_GatherInfo().

◆ m_Quals

TQuals CSourceFeatureItem::m_Quals
mutableprivate

Definition at line 454 of file feature_item.hpp.

Referenced by x_AddQual(), x_FormatQual(), and x_FormatQuals().

◆ m_WasDesc

bool CSourceFeatureItem::m_WasDesc
private

Definition at line 453 of file feature_item.hpp.

Referenced by WasDesc(), and x_FormatNoteQuals().


The documentation for this class was generated from the following files:
Modified on Thu May 23 12:30:17 2024 by modify_doxy.py rev. 669887