NCBI C++ ToolKit
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CEmblGatherer Class Reference

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#include <objtools/format/embl_gather.hpp>

+ Inheritance diagram for CEmblGatherer:
+ Collaboration diagram for CEmblGatherer:

Public Member Functions

 CEmblGatherer (void)
 
virtual void x_DoSingleSection (CBioseqContext &ctx) const
 
- Public Member Functions inherited from CFlatGatherer
virtual void Gather (CFlatFileContext &ctx, CFlatItemOStream &os, bool doNuc=true, bool doProt=true) const
 
virtual void Gather (CFlatFileContext &ctx, CFlatItemOStream &os, const CSeq_entry_Handle &entry, CBioseq_Handle bsh, bool useSeqEntryIndexing, bool doNuc=true, bool doProt=true, bool fasterSets=false) const
 
virtual void SetCanceledCallback (const ICanceled *pCanceledCallback)
 
virtual ~CFlatGatherer (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
 

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 CFlatGatherer
static CFlatGathererNew (CFlatFileConfig::TFormat format)
 
- 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 Types inherited from CFlatGatherer
enum  EGenomeAnnotComment { eGenomeAnnotComment_No = 0 , eGenomeAnnotComment_Yes }
 
typedef CRange< TSeqPosTRange
 
typedef CBioseqContext::TReferences TReferences
 
typedef CRef< CSourceFeatureItemTSFItem
 
typedef deque< TSFItemTSourceFeatSet
 
typedef vector< CRef< CCommentItem > > TCommentVec
 
- Protected Member Functions inherited from CFlatGatherer
 CFlatGatherer ()
 
CFlatItemOStreamItemOS (void) const
 
CBioseqContextContext (void) const
 
const CFlatFileConfigConfig (void) const
 
vector< string > & RefCache (void) const
 
virtual void x_GatherSeqEntry (CFlatFileContext &ctx, CRef< CTopLevelSeqEntryContext > topLevelSeqEntryContext=CRef< CTopLevelSeqEntryContext >(), bool doNuc=true, bool doProt=true) const
 
virtual void x_GatherSeqEntry (CFlatFileContext &ctx, const CSeq_entry_Handle &entry, CBioseq_Handle bsh, bool useSeqEntryIndexing, CRef< CTopLevelSeqEntryContext > topLevelSeqEntryContext=CRef< CTopLevelSeqEntryContext >(), bool doNuc=true, bool doProt=true) const
 
virtual void x_GatherBioseq (const CBioseq_Handle &prev_seq, const CBioseq_Handle &this_seq, const CBioseq_Handle &next_seq, CRef< CTopLevelSeqEntryContext > topLevelSeqEntryContext=CRef< CTopLevelSeqEntryContext >()) const
 
virtual void x_DoMultipleSections (const CBioseq_Handle &seq) const
 
virtual CFeatureItemx_NewFeatureItem (const CMappedFeat &feat, CBioseqContext &ctx, const CSeq_loc *loc, CRef< feature::CFeatTree > ftree, CFeatureItem::EMapped mapped=CFeatureItem::eMapped_not_mapped, bool suppressAccession=false, CConstRef< CFeatureItem > parentFeatureItem=CConstRef< CFeatureItem >()) const
 
void x_GatherSourceOrganism (void) const
 
void x_GatherReferences (void) const
 
void x_GatherReferences (const CSeq_loc &loc, TReferences &refs) const
 
void x_GatherReferencesIdx (const CSeq_loc &loc, TReferences &refs) const
 
void x_GatherCDSReferences (TReferences &refs) const
 
void x_GatherFeatures (void) const
 
void x_GatherFeaturesIdx (void) const
 
void x_GetFeatsOnCdsProduct (const CSeq_feat &feat, CBioseqContext &ctx, CRef< CSeq_loc_Mapper > slice_mapper, CConstRef< CFeatureItem > cdsFeatureItem=CConstRef< CFeatureItem >()) const
 
void x_GetFeatsOnCdsProductIdx (const CSeq_feat &feat, CBioseqContext &ctx, CRef< CSeq_loc_Mapper > slice_mapper, CConstRef< CFeatureItem > cdsFeatureItem=CConstRef< CFeatureItem >()) const
 
void x_CopyCDSFromCDNA (const CSeq_feat &feat, CBioseqContext &ctx) const
 
bool x_SkipFeature (const CSeq_feat &feat, const CBioseqContext &ctx) const
 
virtual void x_GatherFeaturesOnLocation (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const
 
void x_GatherFeaturesOnWholeLocationIdx (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const
 
void x_GatherFeaturesOnWholeLocation (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const
 
void x_GatherFeaturesOnRangeIdx (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const
 
void x_GatherFeaturesOnRange (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const
 
void x_GatherSourceFeatures (void) const
 
void x_CollectBioSources (TSourceFeatSet &srcs) const
 
void x_CollectBioSourcesOnBioseq (const CBioseq_Handle &bh, const TRange &range, CBioseqContext &ctx, TSourceFeatSet &srcs) const
 
void x_CollectSourceDescriptors (const CBioseq_Handle &bh, CBioseqContext &ctx, TSourceFeatSet &srcs) const
 
void x_CollectSourceFeatures (const CBioseq_Handle &bh, const TRange &range, CBioseqContext &ctx, TSourceFeatSet &srcs) const
 
void x_MergeEqualBioSources (TSourceFeatSet &srcs) const
 
bool x_BiosourcesEqualForMergingPurposes (const CSourceFeatureItem &src1, const CSourceFeatureItem &src2) const
 
void x_SubtractFromFocus (TSourceFeatSet &srcs) const
 
void x_GatherAlignments (void) const
 
void x_GatherComments (void) const
 
void x_AddComment (CCommentItem *comment) const
 
void x_AddGSDBComment (const CDbtag &dbtag, CBioseqContext &ctx) const
 
void x_RemoveDupComments (void) const
 
void x_RemoveExcessNewlines (void) const
 
void x_FlushComments (void) const
 
void x_UnverifiedComment (CBioseqContext &ctx) const
 
void x_UnreviewedComment (CBioseqContext &ctx) const
 
void x_AuthorizedAccessComment (CBioseqContext &ctx) const
 
void x_MapComment (CBioseqContext &ctx) const
 
void x_BasemodComment (CBioseqContext &ctx) const
 
void x_IdComments (CBioseqContext &ctx, EGenomeAnnotComment eGenomeAnnotComment) const
 
void x_RefSeqComments (CBioseqContext &ctx, EGenomeAnnotComment eGenomeAnnotComment) const
 
void x_HistoryComments (CBioseqContext &ctx) const
 
void x_RefSeqGenomeComments (CBioseqContext &ctx) const
 
void x_WGSComment (CBioseqContext &ctx) const
 
void x_TSAComment (CBioseqContext &ctx) const
 
void x_TLSComment (CBioseqContext &ctx) const
 
void x_GBBSourceComment (CBioseqContext &ctx) const
 
void x_BarcodeComment (CBioseqContext &ctx) const
 
void x_DescComments (CBioseqContext &ctx) const
 
void x_MaplocComments (CBioseqContext &ctx) const
 
void x_RegionComments (CBioseqContext &ctx) const
 
void x_HTGSComments (CBioseqContext &ctx) const
 
void x_AnnotComments (CBioseqContext &ctx) const
 
CConstRef< CUser_objectx_PrepareAnnotDescStrucComment (CBioseqContext &ctx) const
 
CConstRef< CUser_objectx_GetAnnotDescStrucCommentFromBioseqHandle (CBioseq_Handle bsh) const
 
void x_FeatComments (CBioseqContext &ctx) const
 
void x_NameComments (CBioseqContext &ctx) const
 
void x_StructuredComments (CBioseqContext &ctx) const
 
void x_UnorderedComments (CBioseqContext &ctx) const
 
void x_GatherSequence (void) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Static Protected Member Functions inherited from CFlatGatherer
static void x_GiveOneResidueIntervalsBogusFuzz (CSeq_loc &loc)
 
static void x_RemoveBogusFuzzFromIntervals (CSeq_loc &loc)
 
- Protected Attributes inherited from CFlatGatherer
CRef< CFlatItemOStreamm_ItemOS
 
CRef< CFlatFileContextm_Context
 
CRef< CBioseqContextm_Current
 
TCommentVec m_Comments
 
vector< stringm_RefCache
 
CConstRef< CUser_objectm_FirstGenAnnotSCAD
 
const ICanceledm_pCanceledCallback
 
CRef< feature::CFeatTree > m_Feat_Tree
 
CSeq_entry_Handle m_TopSEH
 

Detailed Description

Definition at line 45 of file embl_gather.hpp.

Constructor & Destructor Documentation

◆ CEmblGatherer()

CEmblGatherer::CEmblGatherer ( void  )

Definition at line 61 of file embl_gather.cpp.

Member Function Documentation

◆ x_DoSingleSection()

void CEmblGatherer::x_DoSingleSection ( CBioseqContext ctx) const
virtual

The documentation for this class was generated from the following files:
Modified on Sun Mar 03 03:11:01 2024 by modify_doxy.py rev. 669887