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CFlatGatherer Class Referenceabstract

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#include <objtools/format/gather_items.hpp>

+ Inheritance diagram for CFlatGatherer:
+ Collaboration diagram for CFlatGatherer:

Public Member Functions

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
 

Static Public Member Functions

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)
 

Protected Types

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

 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 void x_DoSingleSection (CBioseqContext &ctx) const =0
 
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

static void x_GiveOneResidueIntervalsBogusFuzz (CSeq_loc &loc)
 
static void x_RemoveBogusFuzzFromIntervals (CSeq_loc &loc)
 

Protected Attributes

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
 

Private Member Functions

 CFlatGatherer (const CFlatGatherer &)
 
CFlatGathereroperator= (const CFlatGatherer &)
 

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 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 58 of file gather_items.hpp.

Member Typedef Documentation

◆ TCommentVec

typedef vector< CRef<CCommentItem> > CFlatGatherer::TCommentVec
protected

Definition at line 210 of file gather_items.hpp.

◆ TRange

typedef CRange<TSeqPos> CFlatGatherer::TRange
protected

Definition at line 77 of file gather_items.hpp.

◆ TReferences

Definition at line 118 of file gather_items.hpp.

◆ TSFItem

Definition at line 149 of file gather_items.hpp.

◆ TSourceFeatSet

typedef deque<TSFItem> CFlatGatherer::TSourceFeatSet
protected

Definition at line 150 of file gather_items.hpp.

Member Enumeration Documentation

◆ EGenomeAnnotComment

Enumerator
eGenomeAnnotComment_No 
eGenomeAnnotComment_Yes 

Definition at line 168 of file gather_items.hpp.

Constructor & Destructor Documentation

◆ ~CFlatGatherer()

CFlatGatherer::~CFlatGatherer ( void  )
virtual

Definition at line 255 of file gather_items.cpp.

◆ CFlatGatherer() [1/2]

CFlatGatherer::CFlatGatherer ( )
inlineprotected

Definition at line 79 of file gather_items.hpp.

◆ CFlatGatherer() [2/2]

CFlatGatherer::CFlatGatherer ( const CFlatGatherer )
private

Member Function Documentation

◆ Config()

const CFlatFileConfig& CFlatGatherer::Config ( void  ) const
inlineprotected

◆ Context()

CBioseqContext& CFlatGatherer::Context ( void  ) const
inlineprotected

Definition at line 82 of file gather_items.hpp.

References m_Current.

◆ Gather() [1/2]

void CFlatGatherer::Gather ( CFlatFileContext ctx,
CFlatItemOStream os,
bool  doNuc = true,
bool  doProt = true 
) const
virtual

◆ Gather() [2/2]

void CFlatGatherer::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

◆ ItemOS()

CFlatItemOStream& CFlatGatherer::ItemOS ( void  ) const
inlineprotected

◆ New()

CFlatGatherer * CFlatGatherer::New ( CFlatFileConfig::TFormat  format)
static

◆ operator=()

CFlatGatherer& CFlatGatherer::operator= ( const CFlatGatherer )
private

◆ RefCache()

vector<string>& CFlatGatherer::RefCache ( void  ) const
inlineprotected

Definition at line 85 of file gather_items.hpp.

References m_RefCache.

Referenced by x_DoMultipleSections(), and x_GatherBioseq().

◆ SetCanceledCallback()

virtual void CFlatGatherer::SetCanceledCallback ( const ICanceled pCanceledCallback)
inlinevirtual

Definition at line 70 of file gather_items.hpp.

References m_pCanceledCallback.

◆ x_AddComment()

void CFlatGatherer::x_AddComment ( CCommentItem comment) const
protected

◆ x_AddGSDBComment()

void CFlatGatherer::x_AddGSDBComment ( const CDbtag dbtag,
CBioseqContext ctx 
) const
protected

Definition at line 1059 of file gather_items.cpp.

References ctx, and m_Comments.

Referenced by x_IdComments().

◆ x_AnnotComments()

void CFlatGatherer::x_AnnotComments ( CBioseqContext ctx) const
protected

◆ x_AuthorizedAccessComment()

void CFlatGatherer::x_AuthorizedAccessComment ( CBioseqContext ctx) const
protected

◆ x_BarcodeComment()

void CFlatGatherer::x_BarcodeComment ( CBioseqContext ctx) const
protected

◆ x_BasemodComment()

void CFlatGatherer::x_BasemodComment ( CBioseqContext ctx) const
protected

Definition at line 1250 of file gather_items.cpp.

References ctx, CCommentItem::GetStringForBaseMod(), NStr::IsBlank(), and x_AddComment().

Referenced by x_GatherComments().

◆ x_BiosourcesEqualForMergingPurposes()

bool CFlatGatherer::x_BiosourcesEqualForMergingPurposes ( const CSourceFeatureItem src1,
const CSourceFeatureItem src2 
) const
protected

◆ x_CollectBioSources()

void CFlatGatherer::x_CollectBioSources ( TSourceFeatSet srcs) const
protected

◆ x_CollectBioSourcesOnBioseq()

void CFlatGatherer::x_CollectBioSourcesOnBioseq ( const CBioseq_Handle bh,
const TRange range,
CBioseqContext ctx,
TSourceFeatSet srcs 
) const
protected

◆ x_CollectSourceDescriptors()

void CFlatGatherer::x_CollectSourceDescriptors ( const CBioseq_Handle bh,
CBioseqContext ctx,
TSourceFeatSet srcs 
) const
protected

◆ x_CollectSourceFeatures()

void CFlatGatherer::x_CollectSourceFeatures ( const CBioseq_Handle bh,
const TRange range,
CBioseqContext ctx,
TSourceFeatSet srcs 
) const
protected

◆ x_CopyCDSFromCDNA()

void CFlatGatherer::x_CopyCDSFromCDNA ( const CSeq_feat feat,
CBioseqContext ctx 
) const
protected

◆ x_DescComments()

void CFlatGatherer::x_DescComments ( CBioseqContext ctx) const
protected

◆ x_DoMultipleSections()

void CFlatGatherer::x_DoMultipleSections ( const CBioseq_Handle seq) const
protectedvirtual

◆ x_DoSingleSection()

virtual void CFlatGatherer::x_DoSingleSection ( CBioseqContext ctx) const
protectedpure virtual

◆ x_FeatComments()

void CFlatGatherer::x_FeatComments ( CBioseqContext ctx) const
protected

◆ x_FlushComments()

void CFlatGatherer::x_FlushComments ( void  ) const
protected

◆ x_GatherAlignments()

void CFlatGatherer::x_GatherAlignments ( void  ) const
protected

◆ x_GatherBioseq()

void CFlatGatherer::x_GatherBioseq ( const CBioseq_Handle prev_seq,
const CBioseq_Handle this_seq,
const CBioseq_Handle next_seq,
CRef< CTopLevelSeqEntryContext topLevelSeqEntryContext = CRef<CTopLevelSeqEntryContext>() 
) const
protectedvirtual

◆ x_GatherCDSReferences()

void CFlatGatherer::x_GatherCDSReferences ( TReferences refs) const
protected

◆ x_GatherComments()

void CFlatGatherer::x_GatherComments ( void  ) const
protected

◆ x_GatherFeatures()

void CFlatGatherer::x_GatherFeatures ( void  ) const
protected

Definition at line 4202 of file gather_items.cpp.

References CSeq_loc::Assign(), CFlatFileConfig::CopyGeneToCDNA(), ctx, CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, CMolInfo_Base::eBiomol_mRNA, eExtreme_Positional, CSeq_loc_Mapper_Base::eLocationToProduct, CFeatureItem::eMapped_from_cdna, CFeatureItem::eMapped_from_genomic, CFeatureItem::eMapped_from_prot, SAnnotSelector::eOverlap_Intervals, SAnnotSelector::eResolve_TSE, ERR_POST_X, Error(), SAnnotSelector::ExcludeTSE(), CSeq_loc_Mapper_Base::fFuzzOption_CStyle, CSeq_loc_Mapper_Base::fFuzzOption_RemoveLimTlOrTr, CSeq_loc::fMerge_All, CFlatFileConfig::ForGBRelease(), CSeq_loc::fSortAndMerge_All, GetBestGeneForMrna(), CBioseq_Handle::GetBioseqLength(), CSeq_loc::GetId(), CSeq_loc_Base::GetInt(), CMappedFeat::GetLocation(), GetMappedmRNAForProduct(), CSeq_feat_Handle::GetOriginalSeq_feat(), CMappedFeat::GetProduct(), CSeq_interval_Base::GetTo(), CBioseq_Handle::GetTSE_Handle(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsWhole(), m_Current, m_Feat_Tree, m_ItemOS, CSeq_loc_Mapper_Base::Map(), CSeq_loc::Merge(), out(), CConstRef< C, Locker >::Reset(), s_ContainsGaps(), s_IsCircularTopology(), s_SetSelection(), SAnnotSelector::SetByProduct(), CSeq_loc_Mapper_Base::SetFuzzOption(), CSeq_loc::SetInt(), SAnnotSelector::SetLimitNone(), SAnnotSelector::SetLimitTSE(), SAnnotSelector::SetOverlapType(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), SAnnotSelector::SetResolveDepth(), SAnnotSelector::SetResolveMethod(), CSeq_loc::SetWhole(), CFlatFileConfig::UseSeqEntryIndexer(), x_GatherFeaturesIdx(), x_GatherFeaturesOnLocation(), and x_NewFeatureItem().

Referenced by CEmblGatherer::x_DoSingleSection(), CFtableGatherer::x_DoSingleSection(), and CGenbankGatherer::x_DoSingleSection().

◆ x_GatherFeaturesIdx()

void CFlatGatherer::x_GatherFeaturesIdx ( void  ) const
protected

Definition at line 4064 of file gather_items.cpp.

References CSeq_loc::Assign(), CFlatFileConfig::CopyGeneToCDNA(), ctx, CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, CMolInfo_Base::eBiomol_mRNA, eExtreme_Positional, CSeq_loc_Mapper_Base::eLocationToProduct, CFeatureItem::eMapped_from_cdna, CFeatureItem::eMapped_from_genomic, CFeatureItem::eMapped_from_prot, SAnnotSelector::eOverlap_Intervals, SAnnotSelector::eResolve_TSE, ERR_POST_X, Error(), SAnnotSelector::ExcludeTSE(), CSeq_loc_Mapper_Base::fFuzzOption_CStyle, CSeq_loc_Mapper_Base::fFuzzOption_RemoveLimTlOrTr, CSeq_loc::fMerge_All, CFlatFileConfig::ForGBRelease(), CSeq_loc::fSortAndMerge_All, GetBestGeneForMrna(), CSeqEntryIndex::GetBioseqIndex(), CBioseq_Handle::GetBioseqLength(), CSeq_loc::GetId(), CSeq_loc_Base::GetInt(), CMappedFeat::GetLocation(), GetMappedmRNAForProduct(), CSeq_feat_Handle::GetOriginalSeq_feat(), CMappedFeat::GetProduct(), CSeq_interval_Base::GetTo(), CBioseq_Handle::GetTSE_Handle(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsWhole(), m_Current, m_Feat_Tree, m_ItemOS, CSeq_loc_Mapper_Base::Map(), CSeq_loc::Merge(), out(), CConstRef< C, Locker >::Reset(), s_ContainsGaps(), s_IsCircularTopology(), s_SetSelection(), SAnnotSelector::SetByProduct(), CSeq_loc_Mapper_Base::SetFuzzOption(), CSeq_loc::SetInt(), SAnnotSelector::SetLimitNone(), SAnnotSelector::SetLimitTSE(), SAnnotSelector::SetOverlapType(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), SAnnotSelector::SetResolveDepth(), SAnnotSelector::SetResolveMethod(), CSeq_loc::SetWhole(), CFlatFileConfig::UseSeqEntryIndexer(), x_GatherFeaturesOnRangeIdx(), x_GatherFeaturesOnWholeLocationIdx(), and x_NewFeatureItem().

Referenced by x_GatherFeatures().

◆ x_GatherFeaturesOnLocation()

void CFlatGatherer::x_GatherFeaturesOnLocation ( const CSeq_loc loc,
SAnnotSelector sel,
CBioseqContext ctx 
) const
protectedvirtual

◆ x_GatherFeaturesOnRange()

void CFlatGatherer::x_GatherFeaturesOnRange ( const CSeq_loc loc,
SAnnotSelector sel,
CBioseqContext ctx 
) const
protected

Definition at line 3809 of file gather_items.cpp.

References CScope::AddBioseq(), ctx, delta(), eEndsOnBioseqOpt_LastPartOfSeqLoc, eNa_strand_minus, NStr::EqualNocase(), ERR_POST_X, Error(), SAnnotSelector::eSortOrder_Reverse, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gap, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_site, CSeq_feat_Handle::GetData(), CException::GetErrCodeString(), CSeq_feat_Handle::GetFeatSubtype(), GetIdHandle(), CMappedFeat::GetLocation(), CMappedFeat::GetMappedFeature(), CMappedFeat::GetOriginalFeature(), CMappedFeat::GetProduct(), GetResolveOrder(), CMappedFeat::GetSeq_feat_Handle(), CSeq_loc::GetStrand(), CSeq_loc::GetTotalRange(), CFlatFileConfig::HideCDDFeatures(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Handle::IsPlainFeat(), CSeqFeatData_Base::IsRna(), CSeq_feat_Handle::IsSetProduct(), CSeq_loc::IsSetStrand(), kMax_Int, m_Feat_Tree, m_ItemOS, CSeq_loc_Mapper_Base::Map(), out(), prot, compile_time_bits::range(), CScope::RemoveBioseq(), CConstRef< C, Locker >::Reset(), rna, s_CleanCDDFeature(), s_CopyCDSFromCDNA(), s_GetFeatDesc(), s_GetTrimmedMappedFeat(), s_IsCDD(), s_IsDuplicateFeatures(), s_MakeSliceMapper(), s_NormalizeNullsBetween(), s_SeqLocEndsOnBioseq(), SAnnotSelector::SetAdaptiveDepth(), SAnnotSelector::SetIgnoreStrand(), SAnnotSelector::SetResolveAll(), SAnnotSelector::SetResolveDepth(), SAnnotSelector::SetSortOrder(), CException::what(), CSeqFeatData_Base::Which(), x_CopyCDSFromCDNA(), x_GetFeatsOnCdsProduct(), and x_NewFeatureItem().

Referenced by x_GatherFeaturesOnLocation().

◆ x_GatherFeaturesOnRangeIdx()

void CFlatGatherer::x_GatherFeaturesOnRangeIdx ( const CSeq_loc loc,
SAnnotSelector sel,
CBioseqContext ctx 
) const
protected

Definition at line 3584 of file gather_items.cpp.

References ctx, CSeq_id_Base::e_Swissprot, eEndsOnBioseqOpt_LastPartOfSeqLoc, eExtreme_Positional, eNa_strand_minus, NStr::EqualNocase(), ERR_POST_X, Error(), SAnnotSelector::eSortOrder_Reverse, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_site, CSeq_loc::fMerge_Abutting, CSeqEntryIndex::GetBioseqIndex(), CSeq_feat_Handle::GetData(), CSeqMap_CI::GetEndPosition(), CException::GetErrCodeString(), CSeq_feat_Handle::GetFeatSubtype(), CSeq_loc::GetId(), GetIdHandle(), GetLength(), CMappedFeat::GetLocation(), CMappedFeat::GetMappedFeature(), CMappedFeat::GetOriginalFeature(), CSeqMap_CI::GetPosition(), CMappedFeat::GetProduct(), GetResolveOrder(), CBioseqIndex::GetSelector(), CMappedFeat::GetSeq_feat_Handle(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::GetTotalRange(), CFlatFileConfig::HideCDDFeatures(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsRna(), CSeq_feat_Handle::IsSetProduct(), CSeq_loc::IsSetStrand(), m_Feat_Tree, m_ItemOS, CSeq_loc_Mapper_Base::Map(), out(), prot, compile_time_bits::range(), CConstRef< C, Locker >::Reset(), rna, s_CleanCDDFeature(), s_CopyCDSFromCDNA(), s_CreateGapMapIter(), s_GetFeatDesc(), s_GetTrimmedMappedFeat(), s_IsCDD(), s_IsDuplicateFeatures(), s_MakeSliceMapper(), s_NewGapItem(), s_NormalizeNullsBetween(), s_SeqLocEndsOnBioseq(), Seq_loc_Merge(), SAnnotSelector::SetIgnoreStrand(), SAnnotSelector::SetSortOrder(), CException::what(), CSeqFeatData_Base::Which(), x_CopyCDSFromCDNA(), x_GetFeatsOnCdsProduct(), x_GetFeatsOnCdsProductIdx(), and x_NewFeatureItem().

Referenced by x_GatherFeaturesIdx(), and x_GatherFeaturesOnLocation().

◆ x_GatherFeaturesOnWholeLocation()

void CFlatGatherer::x_GatherFeaturesOnWholeLocation ( const CSeq_loc loc,
SAnnotSelector sel,
CBioseqContext ctx 
) const
protected

◆ x_GatherFeaturesOnWholeLocationIdx()

void CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx ( const CSeq_loc loc,
SAnnotSelector sel,
CBioseqContext ctx 
) const
protected

Definition at line 3017 of file gather_items.cpp.

References ctx, CSeqFeatData_Base::e_Cdregion, CSeq_id_Base::e_Swissprot, eEndsOnBioseqOpt_LastPartOfSeqLoc, eExtreme_Positional, CFlatFileConfig::ePolicy_Adaptive, CFlatFileConfig::ePolicy_External, CFlatFileConfig::ePolicy_Web, NStr::EqualNocase(), ERR_POST_X, Error(), CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gap, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_site, CScope::GetBioseqHandles(), CSeqEntryIndex::GetBioseqIndex(), CBioseq_Handle::GetBioseqLength(), CScope::GetCDDAnnots(), CSeq_feat_Handle::GetData(), CException::GetErrCodeString(), CSeq_feat_Handle::GetFeatSubtype(), CBioseqIndex::GetGapIndices(), CSeq_loc::GetId(), GetLength(), CFeatureIndex::GetMappedFeat(), CFeatureIndex::GetMappedLocation(), CConstRef< C, Locker >::GetNonNullPointer(), CBioseq_Handle::GetScope(), CMappedFeat::GetSeq_feat_Handle(), CFeatureIndex::GetSeqFeatHandle(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CFlatFileConfig::HideCDDFeatures(), int, CSeqFeatData_Base::IsCdregion(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPnt(), CFlatFileConfig::IsPolicyGenomes(), CSeq_feat_Handle::IsSetProduct(), CBioseqIndex::IterateFeatures(), m_Feat_Tree, m_ItemOS, SGapIdxData::num_gaps, out(), CConstRef< C, Locker >::Reset(), s_CleanCDDFeature(), s_CopyCDSFromCDNA(), s_CreateGapMapIter(), s_GetFeatDesc(), s_IsCDD(), s_IsDuplicateFeatures(), s_NewGapItem(), s_NormalizeNullsBetween(), s_SeqLocEndsOnBioseq(), s_SetGapIdxData(), SAnnotSelector::SetFeatType(), CException::what(), CSeqFeatData_Base::Which(), x_CopyCDSFromCDNA(), x_GetFeatsOnCdsProductIdx(), and x_NewFeatureItem().

Referenced by x_GatherFeaturesIdx(), and x_GatherFeaturesOnLocation().

◆ x_GatherReferences() [1/2]

void CFlatGatherer::x_GatherReferences ( const CSeq_loc loc,
TReferences refs 
) const
protected

◆ x_GatherReferences() [2/2]

void CFlatGatherer::x_GatherReferences ( void  ) const
protected

◆ x_GatherReferencesIdx()

void CFlatGatherer::x_GatherReferencesIdx ( const CSeq_loc loc,
TReferences refs 
) const
protected

◆ x_GatherSeqEntry() [1/2]

void CFlatGatherer::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
protectedvirtual

◆ x_GatherSeqEntry() [2/2]

void CFlatGatherer::x_GatherSeqEntry ( CFlatFileContext ctx,
CRef< CTopLevelSeqEntryContext topLevelSeqEntryContext = CRef<CTopLevelSeqEntryContext>(),
bool  doNuc = true,
bool  doProt = true 
) const
protectedvirtual

◆ x_GatherSequence()

void CFlatGatherer::x_GatherSequence ( void  ) const
protected

◆ x_GatherSourceFeatures()

void CFlatGatherer::x_GatherSourceFeatures ( void  ) const
protected

◆ x_GatherSourceOrganism()

void CFlatGatherer::x_GatherSourceOrganism ( void  ) const
protected

◆ x_GBBSourceComment()

void CFlatGatherer::x_GBBSourceComment ( CBioseqContext ctx) const
protected

◆ x_GetAnnotDescStrucCommentFromBioseqHandle()

CConstRef< CUser_object > CFlatGatherer::x_GetAnnotDescStrucCommentFromBioseqHandle ( CBioseq_Handle  bsh) const
protected

◆ x_GetFeatsOnCdsProduct()

void CFlatGatherer::x_GetFeatsOnCdsProduct ( const CSeq_feat feat,
CBioseqContext ctx,
CRef< CSeq_loc_Mapper slice_mapper,
CConstRef< CFeatureItem cdsFeatureItem = CConstRef<CFeatureItem>() 
) const
protected

◆ x_GetFeatsOnCdsProductIdx()

void CFlatGatherer::x_GetFeatsOnCdsProductIdx ( const CSeq_feat feat,
CBioseqContext ctx,
CRef< CSeq_loc_Mapper slice_mapper,
CConstRef< CFeatureItem cdsFeatureItem = CConstRef<CFeatureItem>() 
) const
protected

Definition at line 4433 of file gather_items.cpp.

References CFeatTrim::Apply(), CSerialObject::Assign(), ConstRef(), ctx, CSeqFeatData_Base::e_Cdregion, eEndsOnBioseqOpt_AnyPartOfSeqLoc, CFeatureItem::eMapped_from_prot, CSeq_loc_Mapper_Base::eProductToLocation, CSeqFeatData::eSubtype_bond, CSeqFeatData::eSubtype_mat_peptide_aa, CSeqFeatData::eSubtype_preprotein, CSeqFeatData::eSubtype_propeptide_aa, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_sig_peptide_aa, CSeqFeatData::eSubtype_site, CSeqFeatData::eSubtype_transit_peptide_aa, CSeq_loc_Mapper_Base::fFuzzOption_CStyle, CSeq_loc::fMerge_Abutting, CScope::GetBioseqHandle(), CScope::GetBioseqHandleFromTSE(), CSeq_feat_Handle::GetFeatSubtype(), CSeq_feat_Handle::GetLocation(), CMappedFeat::GetMappedFeature(), CMappedFeat::GetOriginalFeature(), CMappedFeat::GetSeq_feat_Handle(), CFlatFileConfig::HideCDDFeatures(), CFlatFileConfig::HideCDSProdFeatures(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsPacked_int(), CFlatFileConfig::IsPolicyFtp(), CFlatFileConfig::IsPolicyGenomes(), CFlatFileConfig::IsPolicyInternal(), CSeq_loc_Mapper_Base::Map(), prev(), prot, compile_time_bits::range(), CSeq_feat_Base::ResetLocation(), s_CleanCDDFeature(), s_GetCdsProductSel(), s_GetTrimmedMappedFeat(), s_IsCDD(), s_IsDuplicateFeatures(), s_NormalizeNullsBetween(), s_SeqLocEndsOnBioseq(), Seq_loc_Merge(), CSeq_loc_Mapper_Base::SetFuzzOption(), CSeq_feat_Base::SetLocation(), and CFlatFileConfig::ShowCDDFeatures().

Referenced by x_GatherFeaturesOnRangeIdx(), and x_GatherFeaturesOnWholeLocationIdx().

◆ x_GiveOneResidueIntervalsBogusFuzz()

void CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz ( CSeq_loc loc)
staticprotected

◆ x_HistoryComments()

void CFlatGatherer::x_HistoryComments ( CBioseqContext ctx) const
protected

◆ x_HTGSComments()

void CFlatGatherer::x_HTGSComments ( CBioseqContext ctx) const
protected

◆ x_IdComments()

void CFlatGatherer::x_IdComments ( CBioseqContext ctx,
EGenomeAnnotComment  eGenomeAnnotComment 
) const
protected

◆ x_MapComment()

void CFlatGatherer::x_MapComment ( CBioseqContext ctx) const
protected

◆ x_MaplocComments()

void CFlatGatherer::x_MaplocComments ( CBioseqContext ctx) const
protected

Definition at line 1570 of file gather_items.cpp.

References ctx, CSeqdesc_Base::e_Maploc, and x_AddComment().

Referenced by x_GatherComments().

◆ x_MergeEqualBioSources()

void CFlatGatherer::x_MergeEqualBioSources ( TSourceFeatSet srcs) const
protected

◆ x_NameComments()

void CFlatGatherer::x_NameComments ( CBioseqContext ctx) const
protected

Definition at line 1586 of file gather_items.cpp.

References ctx, CSeqdesc_Base::e_Name, and x_AddComment().

Referenced by x_GatherComments().

◆ x_NewFeatureItem()

virtual CFeatureItem* CFlatGatherer::x_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
inlineprotectedvirtual

◆ x_PrepareAnnotDescStrucComment()

CConstRef< CUser_object > CFlatGatherer::x_PrepareAnnotDescStrucComment ( CBioseqContext ctx) const
protected

◆ x_RefSeqComments()

void CFlatGatherer::x_RefSeqComments ( CBioseqContext ctx,
EGenomeAnnotComment  eGenomeAnnotComment 
) const
protected

◆ x_RefSeqGenomeComments()

void CFlatGatherer::x_RefSeqGenomeComments ( CBioseqContext ctx) const
protected

◆ x_RegionComments()

void CFlatGatherer::x_RegionComments ( CBioseqContext ctx) const
protected

Definition at line 1578 of file gather_items.cpp.

References ctx, CSeqdesc_Base::e_Region, and x_AddComment().

Referenced by x_GatherComments().

◆ x_RemoveBogusFuzzFromIntervals()

void CFlatGatherer::x_RemoveBogusFuzzFromIntervals ( CSeq_loc loc)
staticprotected

◆ x_RemoveDupComments()

void CFlatGatherer::x_RemoveDupComments ( void  ) const
protected

◆ x_RemoveExcessNewlines()

void CFlatGatherer::x_RemoveExcessNewlines ( void  ) const
protected

Definition at line 1090 of file gather_items.cpp.

References m_Comments, and CCommentItem::RemoveExcessNewlines().

Referenced by x_GatherComments().

◆ x_SkipFeature()

bool CFlatGatherer::x_SkipFeature ( const CSeq_feat feat,
const CBioseqContext ctx 
) const
protected

◆ x_StructuredComments()

void CFlatGatherer::x_StructuredComments ( CBioseqContext ctx) const
protected

◆ x_SubtractFromFocus()

void CFlatGatherer::x_SubtractFromFocus ( TSourceFeatSet srcs) const
protected

◆ x_TLSComment()

void CFlatGatherer::x_TLSComment ( CBioseqContext ctx) const
protected

◆ x_TSAComment()

void CFlatGatherer::x_TSAComment ( CBioseqContext ctx) const
protected

◆ x_UnorderedComments()

void CFlatGatherer::x_UnorderedComments ( CBioseqContext ctx) const
protected

◆ x_UnreviewedComment()

void CFlatGatherer::x_UnreviewedComment ( CBioseqContext ctx) const
protected

◆ x_UnverifiedComment()

void CFlatGatherer::x_UnverifiedComment ( CBioseqContext ctx) const
protected

◆ x_WGSComment()

void CFlatGatherer::x_WGSComment ( CBioseqContext ctx) const
protected

Member Data Documentation

◆ m_Comments

TCommentVec CFlatGatherer::m_Comments
mutableprotected

◆ m_Context

CRef<CFlatFileContext> CFlatGatherer::m_Context
mutableprotected

Definition at line 214 of file gather_items.hpp.

Referenced by Config(), Gather(), x_DoMultipleSections(), and x_GatherBioseq().

◆ m_Current

CRef<CBioseqContext> CFlatGatherer::m_Current
mutableprotected

◆ m_Feat_Tree

CRef<feature::CFeatTree> CFlatGatherer::m_Feat_Tree
mutableprotected

◆ m_FirstGenAnnotSCAD

CConstRef<CUser_object> CFlatGatherer::m_FirstGenAnnotSCAD
mutableprotected

Definition at line 220 of file gather_items.hpp.

Referenced by x_GatherComments(), and x_StructuredComments().

◆ m_ItemOS

CRef<CFlatItemOStream> CFlatGatherer::m_ItemOS
mutableprotected

◆ m_pCanceledCallback

const ICanceled* CFlatGatherer::m_pCanceledCallback
protected

Definition at line 223 of file gather_items.hpp.

Referenced by SetCanceledCallback(), and x_GatherBioseq().

◆ m_RefCache

vector<string> CFlatGatherer::m_RefCache
mutableprotected

Definition at line 218 of file gather_items.hpp.

Referenced by Gather(), and RefCache().

◆ m_TopSEH

CSeq_entry_Handle CFlatGatherer::m_TopSEH
mutableprotected

Definition at line 227 of file gather_items.hpp.

Referenced by x_GatherSeqEntry().


The documentation for this class was generated from the following files:
Modified on Sun Apr 21 03:42:53 2024 by modify_doxy.py rev. 669887