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CAnnotTypes_CI Class Reference

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#include <objmgr/annot_types_ci.hpp>

+ Inheritance diagram for CAnnotTypes_CI:
+ Collaboration diagram for CAnnotTypes_CI:

Public Types

typedef SAnnotSelector::TAnnotType TAnnotType
 
typedef vector< SAnnotTypeSelector > TAnnotTypes
 
typedef set< CAnnotName > TAnnotNames
 

Public Member Functions

 CAnnotTypes_CI (void)
 
 CAnnotTypes_CI (CScope &scope)
 
 CAnnotTypes_CI (TAnnotType type, const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector *params=0)
 
 CAnnotTypes_CI (TAnnotType type, CScope &scope, const CSeq_loc &loc, const SAnnotSelector *params=0)
 
 CAnnotTypes_CI (TAnnotType type, const CSeq_annot_Handle &annot, const SAnnotSelector *params=0)
 
 CAnnotTypes_CI (TAnnotType type, const CSeq_loc &loc, const CSeq_annot_Handle &annot, const SAnnotSelector *params=0)
 
 CAnnotTypes_CI (TAnnotType type, const CSeq_entry_Handle &entry, const SAnnotSelector *params=0)
 
virtual ~CAnnotTypes_CI (void)
 
void Rewind (void)
 
CSeq_annot_Handle GetAnnot (void) const
 
const CSeq_annot_Handle & GetSeq_annot_Handle (void) const
 
size_t GetSize (void) const
 
bool MaxSearchSegmentsLimitIsReached (void) const
 
const TAnnotTypes & GetAnnotTypes (void) const
 
const TAnnotNames & GetAnnotNames (void) const
 
Uint8 GetCostOfLoadingInBytes (void) const
 Get collected cost of loading requested data in bytes. More...
 
double GetCostOfLoadingInSeconds (void) const
 Get collected cost of loading requested data in seconds. More...
 

Protected Types

enum  EAtEnd { at_end }
 
typedef vector< CAnnotObject_Ref > TAnnotSet
 
typedef TAnnotSet::const_iterator TIterator
 

Protected Member Functions

bool IsValid (void) const
 
void Next (void)
 
void Prev (void)
 
const CAnnotObject_Ref & Get (void) const
 
CScope & GetScope (void) const
 
CAnnot_Collector & GetCollector (void)
 
const TIterator & GetIterator (void) const
 
 CAnnotTypes_CI (const CAnnotTypes_CI &src, EAtEnd)
 
bool operator!= (const CAnnotTypes_CI &it) const
 

Private Member Functions

const TAnnotSet & x_GetAnnotSet (void) const
 
void x_Init (CScope &scope, const CSeq_loc &loc, const SAnnotSelector &params)
 

Private Attributes

CRef< CAnnot_Collector > m_DataCollector
 
TIterator m_CurrAnnot
 

Friends

class CAnnot_CI
 
class CTableFieldHandle_Base
 

Detailed Description

Definition at line 50 of file annot_types_ci.hpp.

Member Typedef Documentation

◆ TAnnotNames

typedef set<CAnnotName> CAnnotTypes_CI::TAnnotNames

Definition at line 109 of file annot_types_ci.hpp.

◆ TAnnotSet

typedef vector<CAnnotObject_Ref> CAnnotTypes_CI::TAnnotSet
protected

Definition at line 123 of file annot_types_ci.hpp.

◆ TAnnotType

typedef SAnnotSelector::TAnnotType CAnnotTypes_CI::TAnnotType

Definition at line 53 of file annot_types_ci.hpp.

◆ TAnnotTypes

typedef vector<SAnnotTypeSelector> CAnnotTypes_CI::TAnnotTypes

Definition at line 105 of file annot_types_ci.hpp.

◆ TIterator

typedef TAnnotSet::const_iterator CAnnotTypes_CI::TIterator
protected

Definition at line 124 of file annot_types_ci.hpp.

Member Enumeration Documentation

◆ EAtEnd

enum CAnnotTypes_CI::EAtEnd
protected
Enumerator
at_end 

Definition at line 138 of file annot_types_ci.hpp.

Constructor & Destructor Documentation

◆ CAnnotTypes_CI() [1/8]

CAnnotTypes_CI::CAnnotTypes_CI ( void  )

Definition at line 53 of file annot_types_ci.cpp.

◆ CAnnotTypes_CI() [2/8]

CAnnotTypes_CI::CAnnotTypes_CI ( CScope &  scope)
explicit

Definition at line 60 of file annot_types_ci.cpp.

◆ CAnnotTypes_CI() [3/8]

CAnnotTypes_CI::CAnnotTypes_CI ( TAnnotType  type,
const CBioseq_Handle &  bioseq,
const CRange< TSeqPos > &  range,
ENa_strand  strand,
const SAnnotSelector *  params = 0 
)

Definition at line 97 of file annot_types_ci.cpp.

References SAnnotSelector::CheckAnnotType(), CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::ForceAnnotType(), m_DataCollector, compile_time_bits::range(), Rewind(), and CAnnot_Collector::x_Initialize().

◆ CAnnotTypes_CI() [4/8]

CAnnotTypes_CI::CAnnotTypes_CI ( TAnnotType  type,
CScope &  scope,
const CSeq_loc &  loc,
const SAnnotSelector *  params = 0 
)

Definition at line 155 of file annot_types_ci.cpp.

References SAnnotSelector::CheckAnnotType(), CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::ForceAnnotType(), and x_Init().

◆ CAnnotTypes_CI() [5/8]

CAnnotTypes_CI::CAnnotTypes_CI ( TAnnotType  type,
const CSeq_annot_Handle &  annot,
const SAnnotSelector *  params = 0 
)

Definition at line 176 of file annot_types_ci.cpp.

References SAnnotSelector::ForceAnnotType(), m_DataCollector, Rewind(), SAnnotSelector::SetLimitSeqAnnot(), SAnnotSelector::SetResolveNone(), and CAnnot_Collector::x_Initialize().

◆ CAnnotTypes_CI() [6/8]

CAnnotTypes_CI::CAnnotTypes_CI ( TAnnotType  type,
const CSeq_loc &  loc,
const CSeq_annot_Handle &  annot,
const SAnnotSelector *  params = 0 
)

Definition at line 190 of file annot_types_ci.cpp.

References SAnnotSelector::ForceAnnotType(), CSeq_annot_Handle::GetScope(), SAnnotSelector::SetLimitSeqAnnot(), and x_Init().

◆ CAnnotTypes_CI() [7/8]

CAnnotTypes_CI::CAnnotTypes_CI ( TAnnotType  type,
const CSeq_entry_Handle &  entry,
const SAnnotSelector *  params = 0 
)

Definition at line 203 of file annot_types_ci.cpp.

References SAnnotSelector::eSortOrder_None, SAnnotSelector::ForceAnnotType(), m_DataCollector, Rewind(), SAnnotSelector::SetLimitSeqEntry(), SAnnotSelector::SetResolveNone(), SAnnotSelector::SetSortOrder(), and CAnnot_Collector::x_Initialize().

◆ ~CAnnotTypes_CI()

CAnnotTypes_CI::~CAnnotTypes_CI ( void  )
virtual

Definition at line 224 of file annot_types_ci.cpp.

◆ CAnnotTypes_CI() [8/8]

CAnnotTypes_CI::CAnnotTypes_CI ( const CAnnotTypes_CI &  src,
EAtEnd   
)
inlineprotected

Definition at line 141 of file annot_types_ci.hpp.

Member Function Documentation

◆ Get()

const CAnnotObject_Ref & CAnnotTypes_CI::Get ( void  ) const
inlineprotected

Definition at line 204 of file annot_types_ci.hpp.

References _ASSERT, IsValid(), and m_CurrAnnot.

Referenced by GetAnnot(), CSeq_table_CI::GetMappedLocation(), CAlign_CI::GetOriginalSeq_align(), GetSeq_annot_Handle(), CSeq_table_CI::IsMapped(), CAlign_CI::operator*(), CTableFieldHandle_Base::x_FindColumn(), CTableFieldHandle_Base::x_GetColumn(), and CTableFieldHandle_Base::x_GetRow().

◆ GetAnnot()

CSeq_annot_Handle CAnnotTypes_CI::GetAnnot ( void  ) const

Definition at line 218 of file annot_types_ci.cpp.

References Get(), and CAnnotObject_Ref::GetSeq_annot_Handle().

Referenced by CGraphUtils::CalcGraphLevels(), CSGAlignmentDS::GetDataLoader(), CSeq_table_CI::GetOriginalLocation(), CAlign_CI::GetSeq_align_Handle(), CFeatIdRemapper::RemapId(), CDemoApp::Run(), CSGAlignStatJob::x_CollectAlignStats(), CSGAlignStatJob::x_Execute(), CSGAlignmentJob::x_LoadAlignments(), CSGAlignStatJob::x_LoadAlignments(), CSGSeqGraphJob::x_LoadSeqTable(), and CGff3Writer::xWriteFeature().

◆ GetAnnotNames()

const CAnnotTypes_CI::TAnnotNames & CAnnotTypes_CI::GetAnnotNames ( void  ) const

Definition at line 236 of file annot_types_ci.cpp.

References m_DataCollector, and CAnnot_Collector::x_GetAnnotNames().

Referenced by CGraphUtils::CalcGraphLevels(), CSGFeatureJob::GetAnnotNames(), CSGSegmentSmearJob::GetAnnotNames(), CSGAlignmentJob::GetAnnotNames(), CSGSeqGraphJob::GetAnnotNames(), CEpigenomicsDS::GetAnnotNames(), CSGSnpDS::GetAnnotNames(), CSGFeatureJob::GetAnnotNames_var(), NSnpAnnot::GetGraph_CI(), CBinsDS::GetTrackNames(), CSGHapmapDS::GetTrackNames(), CLDBlockDS::GetTrackNames(), CDemoApp::Run(), CSnpJob::x_FetchGraphs(), CAlignTabExportPage2::x_StartAlignNamesJob(), and CAlignTabExportPage2::x_StartNAAlignNamesJob().

◆ GetAnnotTypes()

const CAnnotTypes_CI::TAnnotTypes & CAnnotTypes_CI::GetAnnotTypes ( void  ) const

Definition at line 230 of file annot_types_ci.cpp.

References m_DataCollector, and CAnnot_Collector::x_GetAnnotTypes().

Referenced by CDemoApp::Run().

◆ GetCollector()

CAnnot_Collector & CAnnotTypes_CI::GetCollector ( void  )
inlineprotected

Definition at line 212 of file annot_types_ci.hpp.

References _ASSERT, and m_DataCollector.

Referenced by CFeat_CI::Update(), CFeat_CI::x_AddFeatures(), and CGraph_CI::x_Update().

◆ GetCostOfLoadingInBytes()

Uint8 CAnnotTypes_CI::GetCostOfLoadingInBytes ( void  ) const
inline

Get collected cost of loading requested data in bytes.

See also
SAnnotSelector::SetCollectCostOfLoading()

Definition at line 249 of file annot_types_ci.hpp.

References m_DataCollector, and CAnnot_Collector::x_GetCostOfLoadingInBytes().

Referenced by CDemoApp::Run().

◆ GetCostOfLoadingInSeconds()

double CAnnotTypes_CI::GetCostOfLoadingInSeconds ( void  ) const
inline

Get collected cost of loading requested data in seconds.

See also
SAnnotSelector::SetCollectCostOfLoading()

Definition at line 256 of file annot_types_ci.hpp.

References m_DataCollector, and CAnnot_Collector::x_GetCostOfLoadingInSeconds().

Referenced by CSGAlignmentDS::GetAlignmentCost(), CSGAlignmentDS::GetGraphCost(), and CDemoApp::Run().

◆ GetIterator()

const CAnnotTypes_CI::TIterator & CAnnotTypes_CI::GetIterator ( void  ) const
inlineprotected

Definition at line 220 of file annot_types_ci.hpp.

References _ASSERT, IsValid(), and m_CurrAnnot.

Referenced by CAlign_CI::GetSeq_align_Handle(), CFeat_CI::Update(), and CGraph_CI::x_Update().

◆ GetScope()

CScope & CAnnotTypes_CI::GetScope ( void  ) const
inlineprotected

Definition at line 241 of file annot_types_ci.hpp.

References _ASSERT, CAnnot_Collector::GetScope(), and m_DataCollector.

◆ GetSeq_annot_Handle()

const CSeq_annot_Handle & CAnnotTypes_CI::GetSeq_annot_Handle ( void  ) const
inline

Definition at line 228 of file annot_types_ci.hpp.

References Get(), and CAnnotObject_Ref::GetSeq_annot_Handle().

◆ GetSize()

size_t CAnnotTypes_CI::GetSize ( void  ) const
inline

Definition at line 235 of file annot_types_ci.hpp.

References x_GetAnnotSet().

Referenced by NSnpAnnot::EstimateSNPCount(), CSGAlignmentJob::GetAlignType(), CSGAlignmentDS::GetDataLoader(), GetMrnasForGene(), CSGSequenceDS::IsPopSet(), NSnp::IsSnpKnown(), CTabularFormatter_ProtRef::Print(), CSeq_annot_EditHandle::ReorderFtable(), CFeatCompareJob_Align::Run(), CFeatCompareJob_Location::Run(), CFeatureRetrievalJob::Run(), CDemoApp::Run(), CFeatTreeSampleApp::Run(), CTestTranscript_CountCdregions::RunTest(), s_HasAlignment(), CSGAlignStatJob::x_CollectAlignStats(), CFeatureGenerator::SImplementation::x_ConstructRnaName(), CSGFeatureJob::x_CreateFeatures(), CGeneModelFeatJob::x_CreateFeaturesWithFilter(), CFeatureGenerator::SImplementation::x_CreateGeneFeature(), CSGFeatureJob::x_Execute(), CGeneModelFeatJob::x_Execute(), CSGAlignmentJob::x_GetAlignments(), CSGAlignmentJob::x_GetAlignSmear(), CSGAlignmentJob::x_LoadAlignmentFeats(), CSGAlignmentJob::x_LoadAlignments(), CSGAlignStatJob::x_LoadAlignments(), CBatchFeatJob::x_LoadFeatProducts(), CLDBlockJob::x_LoadFtable(), CSGAlnQualityScore::x_RetrieveQualityMap(), and CFeatureSearchJob::x_SearchFeatures().

◆ IsValid()

bool CAnnotTypes_CI::IsValid ( void  ) const
inlineprotected

Definition at line 176 of file annot_types_ci.hpp.

References m_CurrAnnot, m_DataCollector, and x_GetAnnotSet().

Referenced by Get(), GetIterator(), CFeat_CI::Update(), and CGraph_CI::x_Update().

◆ MaxSearchSegmentsLimitIsReached()

bool CAnnotTypes_CI::MaxSearchSegmentsLimitIsReached ( void  ) const

Definition at line 242 of file annot_types_ci.cpp.

References m_DataCollector, and CAnnot_Collector::x_MaxSearchSegmentsLimitIsReached().

Referenced by CDemoApp::Run().

◆ Next()

void CAnnotTypes_CI::Next ( void  )
inlineprotected

Definition at line 190 of file annot_types_ci.hpp.

References m_CurrAnnot.

Referenced by CAlign_CI::operator++(), CFeat_CI::operator++(), CGraph_CI::operator++(), and CSeq_table_CI::operator++().

◆ operator!=()

bool CAnnotTypes_CI::operator!= ( const CAnnotTypes_CI &  it) const
inlineprotected

Definition at line 145 of file annot_types_ci.hpp.

References m_CurrAnnot.

Referenced by CAlign_CI::operator!=(), CFeat_CI::operator!=(), CGraph_CI::operator!=(), and CSeq_table_CI::operator!=().

◆ Prev()

void CAnnotTypes_CI::Prev ( void  )
inlineprotected

Definition at line 197 of file annot_types_ci.hpp.

References m_CurrAnnot.

Referenced by CAlign_CI::operator--(), CFeat_CI::operator--(), CGraph_CI::operator--(), and CSeq_table_CI::operator--().

◆ Rewind()

void CAnnotTypes_CI::Rewind ( void  )
inline

Definition at line 183 of file annot_types_ci.hpp.

References m_CurrAnnot, and x_GetAnnotSet().

Referenced by CAnnotTypes_CI(), CAlign_CI::Rewind(), CFeat_CI::Rewind(), CGraph_CI::Rewind(), and x_Init().

◆ x_GetAnnotSet()

const CAnnotTypes_CI::TAnnotSet & CAnnotTypes_CI::x_GetAnnotSet ( void  ) const
inlineprivate

Definition at line 168 of file annot_types_ci.hpp.

References _ASSERT, CAnnot_Collector::GetAnnotSet(), and m_DataCollector.

Referenced by GetSize(), IsValid(), and Rewind().

◆ x_Init()

void CAnnotTypes_CI::x_Init ( CScope &  scope,
const CSeq_loc &  loc,
const SAnnotSelector &  params 
)
private

Definition at line 121 of file annot_types_ci.cpp.

References CHandleRangeMap::AddLocation(), eNa_strand_unknown, CScope::GetBioseqHandle(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::GetWhole(), CSeq_loc_Base::IsInt(), CSeq_interval_Base::IsSetStrand(), CSeq_loc_Base::IsWhole(), m_DataCollector, compile_time_bits::range(), Rewind(), and CAnnot_Collector::x_Initialize().

Referenced by CAnnotTypes_CI().

Friends And Related Function Documentation

◆ CAnnot_CI

friend class CAnnot_CI
friend

Definition at line 120 of file annot_types_ci.hpp.

◆ CTableFieldHandle_Base

friend class CTableFieldHandle_Base
friend

Definition at line 121 of file annot_types_ci.hpp.

Member Data Documentation

◆ m_CurrAnnot

TIterator CAnnotTypes_CI::m_CurrAnnot
private

Definition at line 158 of file annot_types_ci.hpp.

Referenced by Get(), GetIterator(), IsValid(), Next(), operator!=(), Prev(), and Rewind().

◆ m_DataCollector

CRef<CAnnot_Collector> CAnnotTypes_CI::m_DataCollector
private

Definition at line 156 of file annot_types_ci.hpp.

Referenced by CAnnotTypes_CI(), GetAnnotNames(), GetAnnotTypes(), GetCollector(), GetCostOfLoadingInBytes(), GetCostOfLoadingInSeconds(), GetScope(), IsValid(), MaxSearchSegmentsLimitIsReached(), x_GetAnnotSet(), x_Init(), and CAnnot_CI::x_Initialize().

The documentation for this class was generated from the following files:
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