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Represents ASN.1 type Seq-annot defined in file seq.asn

Search Toolkit Book for CSeq_annot_Base

features in table form More...

#include <objects/seq/Seq_annot_.hpp>

+ Inheritance diagram for CSeq_annot_Base:
+ Collaboration diagram for CSeq_annot_Base:

Classes

class  C_Data
 C_Data –. More...
 

Public Types

enum  EDb {
  eDb_genbank = 1, eDb_embl = 2, eDb_ddbj = 3, eDb_pir = 4,
  eDb_sp = 5, eDb_bbone = 6, eDb_pdb = 7, eDb_other = 255
}
 source of annotation More...
 
typedef list< CRef< CAnnot_id > > TId
 
typedef int TDb
 
typedef string TName
 
typedef CAnnot_descr TDesc
 
typedef C_Data TData
 
- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CSeq_annot_Base (void)
 
virtual ~CSeq_annot_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetId (void) const
 Check if a value has been assigned to Id data member. More...
 
bool CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void ResetId (void)
 Reset Id data member. More...
 
const TIdGetId (void) const
 Get the Id member data. More...
 
TIdSetId (void)
 Assign a value to Id data member. More...
 
bool IsSetDb (void) const
 Check if a value has been assigned to Db data member. More...
 
bool CanGetDb (void) const
 Check if it is safe to call GetDb method. More...
 
void ResetDb (void)
 Reset Db data member. More...
 
TDb GetDb (void) const
 Get the Db member data. More...
 
void SetDb (TDb value)
 Assign a value to Db data member. More...
 
TDbSetDb (void)
 Assign a value to Db data member. More...
 
bool IsSetName (void) const
 source if "other" above Check if a value has been assigned to Name data member. More...
 
bool CanGetName (void) const
 Check if it is safe to call GetName method. More...
 
void ResetName (void)
 Reset Name data member. More...
 
const TNameGetName (void) const
 Get the Name member data. More...
 
void SetName (const TName &value)
 Assign a value to Name data member. More...
 
TNameSetName (void)
 Assign a value to Name data member. More...
 
bool IsSetDesc (void) const
 used only for stand alone Seq-annots Check if a value has been assigned to Desc data member. More...
 
bool CanGetDesc (void) const
 Check if it is safe to call GetDesc method. More...
 
void ResetDesc (void)
 Reset Desc data member. More...
 
const TDescGetDesc (void) const
 Get the Desc member data. More...
 
void SetDesc (TDesc &value)
 Assign a value to Desc data member. More...
 
TDescSetDesc (void)
 Assign a value to Desc data member. More...
 
bool IsSetData (void) const
 Check if a value has been assigned to Data data member. More...
 
bool CanGetData (void) const
 Check if it is safe to call GetData method. More...
 
void ResetData (void)
 Reset Data data member. More...
 
const TDataGetData (void) const
 Get the Data member data. More...
 
void SetData (TData &value)
 Assign a value to Data data member. More...
 
TDataSetData (void)
 Assign a value to Data data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (void) const =0
 
virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
 Set object to copy of another one. More...
 
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
 Check if both objects contain the same values. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
void ThrowUnassigned (TMemberIndex index) const
 
void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
 
bool HasNamespaceName (void) const
 Check if object data type has namespace name. More...
 
const stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (void) const
 Get namespace prefix. More...
 
- 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...
 
- 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 const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EDb (void)
 Access to EDb's attributes (values, names) as defined in spec. More...
 
- Static Public Member Functions inherited from CSerialObject
static void SetVerifyDataThread (ESerialVerifyData verify)
 
static void SetVerifyDataGlobal (ESerialVerifyData verify)
 
static string UnassignedString (void)
 
static CStringUTF8 UnassignedStringUTF8 (void)
 
static char UnassignedByte (void)
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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)
 

Private Types

typedef CSerialObject Tparent
 

Private Member Functions

 CSeq_annot_Base (const CSeq_annot_Base &)
 
CSeq_annot_Baseoperator= (const CSeq_annot_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
list< CRef< CAnnot_id > > m_Id
 
int m_Db
 
string m_Name
 
CRef< TDescm_Desc
 
CRef< TDatam_Data
 

Additional Inherited Members

- Static Public Attributes inherited from CSerialObject
static const char * ms_UnassignedStr = "<*unassigned*>"
 
static const char ms_UnassignedByte = char(0xcd)
 
- 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 CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

features in table form

CSeq_annot_Base

Definition at line 85 of file Seq_annot_.hpp.

Member Typedef Documentation

Definition at line 360 of file Seq_annot_.hpp.

Definition at line 357 of file Seq_annot_.hpp.

Definition at line 359 of file Seq_annot_.hpp.

typedef list< CRef< CAnnot_id > > CSeq_annot_Base::TId

Definition at line 356 of file Seq_annot_.hpp.

Definition at line 358 of file Seq_annot_.hpp.

Definition at line 87 of file Seq_annot_.hpp.

Constructor & Destructor Documentation

END_CLASS_INFO CSeq_annot_Base::CSeq_annot_Base ( void  )

Definition at line 271 of file Seq_annot_.cpp.

References CObject::IsAllocatedInPool(), m_set_State, and ResetData().

CSeq_annot_Base::~CSeq_annot_Base ( void  )
virtual

Definition at line 281 of file Seq_annot_.cpp.

CSeq_annot_Base::CSeq_annot_Base ( const CSeq_annot_Base )
private

Member Function Documentation

bool CSeq_annot_Base::CanGetData ( void  ) const
inline

Check if it is safe to call GetData method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 848 of file Seq_annot_.hpp.

Referenced by s_GetSeqAnnotChoiceMask(), CFormatGuessEx::x_TryBed15(), and CFormatGuessEx::x_TryWiggle().

bool CSeq_annot_Base::CanGetDb ( void  ) const
inline

Check if it is safe to call GetDb method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 740 of file Seq_annot_.hpp.

References IsSetDb().

Referenced by GetDb(), and CSeq_annot_Handle::Seq_annot_CanGetDb().

bool CSeq_annot_Base::CanGetDesc ( void  ) const
inline
bool CSeq_annot_Base::CanGetId ( void  ) const
inline

Check if it is safe to call GetId method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 715 of file Seq_annot_.hpp.

Referenced by s_AnnotId(), CGff2Reader::s_GetAnnotId(), CSeq_annot_Handle::Seq_annot_CanGetId(), and CGvfReader::x_GetAnnotById().

bool CSeq_annot_Base::CanGetName ( void  ) const
inline

Check if it is safe to call GetName method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 787 of file Seq_annot_.hpp.

References IsSetName().

Referenced by GetName(), and CSeq_annot_Handle::Seq_annot_CanGetName().

CSeq_annot_Base::DECLARE_INTERNAL_TYPE_INFO ( )
static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME() CSeq_annot_Base::EDb ( void  )
static

Access to EDb's attributes (values, names) as defined in spec.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), and ResetDb().

const CSeq_annot_Base::TData & CSeq_annot_Base::GetData ( void  ) const
inline

Get the Data member data.

Returns
Reference to the member data.

Definition at line 854 of file Seq_annot_.hpp.

References m_Data, and ResetData().

Referenced by AlignmentCollection::addPendingAlignment(), CRemoveSeqAnnot::ApplyToSeqAnot(), BOOST_AUTO_TEST_CASE(), CTestBlastp::CanTest(), Convert_Seq_annot_Seq_align(), Convert_Seq_annot_Seq_feat(), Convert_Seq_annot_Seq_graph(), Convert_Seq_annot_Seq_id(), Convert_Seq_annot_Seq_loc_All(), Convert_Seq_annot_Seq_loc_TotalRange(), CBlobSplitterImpl::CopyAnnot(), CVariationUtilities::CorrectRefAllele(), CSeq_annot_SplitInfo::CountAnnotObjects(), CTableDataSeq_annot::CreateObject(), CTableDataAlnSummary::CTableDataAlnSummary(), DemoteCDSToNucSeq(), CMAViewManager::DoTransition(), EraseRow(), C5ColObjectLoader::Execute(), CDataTrackUtils::GetColumnHeader(), AnnotObjTrait< CSeq_feat >::GetCont(), AnnotObjTrait< CSeq_align >::GetCont(), AnnotObjTrait< CSeq_graph >::GetCont(), GetDenDiagSet(), CDesktopAnnotItem::GetDescription(), CDataTrackUtils::GetFeatSubtypes(), CGuiObjectInfoSeq_annot::GetIcon(), GetInteractionDataFromIbis(), CSeq_annotHandler::GetLabel(), CNAUtils::GetNATrackInfo(), CAnnotationLoader::GetNextAnnot(), CCdCore::GetNumRows(), CSeq_annot_Handle::GetSeq_tableNumRows(), CGuiObjectInfoSeq_annot::GetSubtype(), CGffRecord::GetSubtypeOf(), CGuiObjectInfoSeq_annot::GetViewCategory(), CTableDataFTable::Init(), CSeq_annot::IsAlign(), CSeq_annot_Handle::IsAlign(), CSeq_annot::IsFtable(), CSeq_annot_Handle::IsFtable(), CSeq_annot::IsGraph(), CSeq_annot_Handle::IsGraph(), CSeq_annot::IsIds(), CSeq_annot_Handle::IsIds(), CSeq_annot::IsLocs(), CSeq_annot_Handle::IsLocs(), CSeq_annot::IsSeq_table(), CSeq_annot_Handle::IsSeq_table(), CWriteUtil::IsThreeFeatFormat(), CMultiReader::LoadAnnot(), CSNPSeqInfo::LoadAnnotBlob(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CMakeCdrProds::MakeCdrProds(), CBlobSplitterImpl::MakeID2Chunk(), CBlobSplitterImpl::MakeSeq_annot(), CSeq_loc_Mapper_Base::Map(), CMAViewManager::NeedAnchorPanel(), CAnalyzeShiftApp::ProcessHGVS(), PromoteCDSToNucProtSet(), CPromote::PromoteFeatures(), CGFFReader::Read(), CFeature_table_reader::ReadSequinFeatureTables(), ReadTabDelimitedTable(), CEditsSaver::Remove(), CGeneModelDemoApp::Run(), CTestProtProd_Cdd::RunTest(), CTestBlastp_All::RunTest(), s_AttachAnnotToScope(), s_GetAnnotContent(), s_GetAnnotId(), s_GetAnnotType(), s_GetClipLoc(), s_GetSeqAnnotChoiceMask(), s_ReadMultipleTablesFromString(), UpdateViewer::SaveAlignments(), CClippedScorer::ScoreAlignments(), CRemoveSeqFromAlignDlg::SearchSeq_entry(), SetDenDiagSet(), CSeq_annot_SplitInfo::SetSeq_annot(), CNewCleanup_imp::ShouldRemoveAnnot(), CMytestApplication::TestFeatureGeneOverlap(), CValidError_feat::ValidateSeqFeatXref(), CSeq_annot_Handle::Which(), CUCSCRegionWriter::WriteAnnot(), CGFFReader::x_CreateGeneFeatures(), CBLASTSeqToolJob::x_CreateProjectItems(), CGroupAlignmentsJob::x_CreateProjectItems(), CImportFeatTable::x_DoImportFeaturesFromFile(), CProjectFileWriter::x_GetAnnotId(), CMatchTabulate::x_GetQuery(), CMatchTabulate::x_GetSubject(), CCreateGeneModelTask::x_Group_By_GeneID(), CMatchTabulate::x_HasCdsQuery(), CMatchTabulate::x_HasCdsSubject(), CSeq_annot_Info::x_InitAnnotList(), CMatchTabulate::x_IsCdsComparison(), CMatchTabulate::x_IsComparison(), CID2SNPProcessor_Impl::x_LoadBlob(), CSGSegmentSmearJob::x_LoadFromNA(), CBamRefSeqInfo::x_LoadRangesCov(), CWiggleExportJob::x_RecalculateGraph(), CVariationNormalization_base< T >::x_Shift(), CSplitDataLoader::x_SplitAligns(), CSplitDataLoader::x_SplitAnnot(), CSplitDataLoader::x_SplitFeats(), CSplitDataLoader::x_SplitGraphs(), CCreateGeneModelTask::x_StoreGeneratedFeats(), CFormatGuessEx::x_TryBed15(), CFormatGuessEx::x_TryWiggle(), CModifySeqId::x_UpdateSeqAnnot(), CGff2Reader::xAssignAnnotId(), CMultiReaderApp::xProcess5ColFeatTable(), CBedGraphWriter::xWriteAnnotFeatureTable(), CWiggleWriter::xWriteAnnotGraphs(), CBedGraphWriter::xWriteAnnotGraphs(), CBedGraphWriter::xWriteAnnotSeqTable(), and CWiggleWriter::xWriteAnnotTable().

CSeq_annot_Base::TDb CSeq_annot_Base::GetDb ( void  ) const
inline

Get the Db member data.

Returns
Copy of the member data.

Definition at line 753 of file Seq_annot_.hpp.

References CanGetDb(), m_Db, and CSerialObject::ThrowUnassigned().

Referenced by CBlobSplitterImpl::MakeSeq_annot(), and CSeq_annot_Handle::Seq_annot_GetDb().

const CSeq_annot_Base::TDesc & CSeq_annot_Base::GetDesc ( void  ) const
inline
const CSeq_annot_Base::TId & CSeq_annot_Base::GetId ( void  ) const
inline
const CSeq_annot_Base::TName & CSeq_annot_Base::GetName ( void  ) const
inline
bool CSeq_annot_Base::IsSetData ( void  ) const
inline

Check if a value has been assigned to Data data member.

Data member Data is mandatory; its type is defined as 'typedef C_Data TData'

Returns
  • true, if a value has been assigned.
  • false, otherwise.

Definition at line 842 of file Seq_annot_.hpp.

References m_Data.

Referenced by CTableAnnotDataSource::AddSeqLoc(), CTableAnnotDataSource::AddSnpSeqLoc(), subfuse::CSubmissionCollector::AdjustLocalIds(), CRemoveSeqAnnot::ApplyToSeqAnot(), CAutogeneratedCleanup::BasicCleanupSeqAnnot(), Convert_Seq_annot_Seq_align(), Convert_Seq_annot_Seq_feat(), Convert_Seq_annot_Seq_graph(), CVariationUtilities::CorrectRefAllele(), CTableAnnotDataSource::CreateFeature(), CTableAnnotDataSource::CreateSnpFeature(), CTableAnnotDataSource::CreateSnps(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqAnnot(), CTableAnnotDataSource::FindLocations(), CVDBGraphSeqIterator::GetAnnot(), AnnotObjTrait< CSeq_feat >::GetCont(), AnnotObjTrait< CSeq_align >::GetCont(), AnnotObjTrait< CSeq_graph >::GetCont(), CDesktopAnnotItem::GetDescription(), CAnnotationLoader::GetNextAnnot(), CSeq_annot::IsAlign(), CSeq_annot::IsFtable(), CSeq_annot::IsGraph(), CSeq_annot::IsIds(), CSeq_annot::IsLocs(), CSeq_annot::IsSeq_table(), CTableAnnotDataSource::RemoveSeqLocs(), s_GetSeqAnnotChoiceMask(), s_LoadSeqAnnot(), s_SetSearchParam(), CRemoveSeqFromAlignDlg::SearchSeq_entry(), CNewCleanup_imp::ShouldRemoveAnnot(), CMytestApplication::TestFeatureGeneOverlap(), CUCSCRegionWriter::WriteAnnot(), CAutogeneratedCleanup::x_BasicCleanupBioseq_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_data_annots_E_E(), CCreateGeneModelTask::x_GetCommand(), CVariationNormalization_base< T >::x_Shift(), and CModifySeqId::x_UpdateSeqAnnot().

bool CSeq_annot_Base::IsSetDb ( void  ) const
inline

Check if a value has been assigned to Db data member.

Data member Db is optional; its type is defined as 'typedef int TDb'

Returns
  • true, if a value has been assigned.
  • false, otherwise.

Definition at line 734 of file Seq_annot_.hpp.

References m_set_State.

Referenced by CanGetDb(), CBlobSplitterImpl::MakeSeq_annot(), s_IsMergeableFeatureTable(), CSeq_annot_Handle::Seq_annot_IsSetDb(), and SetDb().

bool CSeq_annot_Base::IsSetDesc ( void  ) const
inline
bool CSeq_annot_Base::IsSetId ( void  ) const
inline

Check if a value has been assigned to Id data member.

Data member Id is optional; its type is defined as 'typedef list< CRef< CAnnot_id > > TId'

Returns
  • true, if a value has been assigned.
  • false, otherwise.

Definition at line 709 of file Seq_annot_.hpp.

References m_set_State.

Referenced by CSeq_annot_SplitInfo::GetName(), CMultiReader::LoadAnnot(), CBlobSplitterImpl::MakeSeq_annot(), s_IsMergeableFeatureTable(), CSeq_annot_Handle::Seq_annot_IsSetId(), and CSeq_annot_Info::x_UpdateName().

bool CSeq_annot_Base::IsSetName ( void  ) const
inline

source if "other" above Check if a value has been assigned to Name data member.

Data member Name is optional; its type is defined as 'typedef string TName'

Returns
  • true, if a value has been assigned.
  • false, otherwise.

Definition at line 781 of file Seq_annot_.hpp.

References m_set_State.

Referenced by CanGetName(), CBlobSplitterImpl::MakeSeq_annot(), s_IsMergeableFeatureTable(), CSeq_annot_Handle::Seq_annot_IsSetName(), SetName(), and CMatchTabulate::x_IsComparison().

CSeq_annot_Base& CSeq_annot_Base::operator= ( const CSeq_annot_Base )
private
void CSeq_annot_Base::Reset ( void  )
virtual

Reset the whole object.

Definition at line 248 of file Seq_annot_.cpp.

References ResetData(), ResetDb(), ResetDesc(), ResetId(), and ResetName().

Referenced by GetInteractionDataFromIbis(), CRmReader::Read(), and CSeq_annot_Base::C_Data::~C_Data().

void CSeq_annot_Base::ResetData ( void  )

Reset Data data member.

Definition at line 234 of file Seq_annot_.cpp.

References m_Data.

Referenced by CSeq_annot_Base(), GetData(), Reset(), and SetData().

void CSeq_annot_Base::ResetDb ( void  )
inline

Reset Db data member.

Definition at line 746 of file Seq_annot_.hpp.

References EDb(), m_Db, and m_set_State.

Referenced by Reset().

void CSeq_annot_Base::ResetDesc ( void  )

Reset Desc data member.

Definition at line 217 of file Seq_annot_.cpp.

References m_Desc.

Referenced by Reset().

void CSeq_annot_Base::ResetId ( void  )

Reset Id data member.

Definition at line 205 of file Seq_annot_.cpp.

References m_Id, and m_set_State.

Referenced by Reset().

void CSeq_annot_Base::ResetName ( void  )

Reset Name data member.

Definition at line 211 of file Seq_annot_.cpp.

References m_Name, and m_set_State.

Referenced by Reset(), and CGroupAlignmentsJob::x_CreateProjectItems().

void CSeq_annot_Base::SetData ( CSeq_annot_Base::TData value)

Assign a value to Data data member.

Parameters
valueReference to value.

Definition at line 243 of file Seq_annot_.cpp.

References m_Data.

Referenced by CFeatureTableReader::_ParseCdregions(), SSeqTableConverter::Add(), AddFeat(), AddFeatureToBioseq(), Sequence::AddMMDBAnnotTag(), AlignmentCollection::addPendingAlignment(), CGBProjectHelper::AddProjectItemsFromRID(), CTableAnnotDataSource::AddSeqLoc(), CTableAnnotDataSource::AddSnpSeqLoc(), AddSpanningSentinelFeat(), subfuse::CSubmissionCollector::AdjustLocalIds(), CVariationNormalization::AlterToDelIns(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CUpdateAlign::apply(), CSourceModParser::ApplyAllMods(), CApplyObject::ApplyChange(), CAttachedHandles::Attach(), CAutogeneratedCleanup::BasicCleanupSeqAnnot(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CTableImportDataSource::ConvertToSeqAnnot(), CVariationUtilities::CorrectRefAllele(), CEntrezDB::CreateAnnot_Nuc_Prot(), CTableAnnotDataSource::CreateFeature(), AlignmentSet::CreateFromMultiple(), CPhrap_Seq::CreatePadsFeat(), CBlastFormatUtil::CreateSeqAnnotFromSeqAlignSet(), CTableAnnotDataSource::CreateSnpFeature(), CTableAnnotDataSource::CreateSnps(), CSourceFeatureItem::CSourceFeatureItem(), DemoteCDSToNucSeq(), CAddFeatChecker::Do(), CMAViewManager::DoTransition(), CWig2tableApplication::DumpChromValues(), CAnnotationASN1::CImplementationData::DumpEvidence(), CCdCore::EraseOtherRows(), EraseRow(), CCreateCoverageTask::Execute(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqAnnot(), CTableAnnotDataSource::FindLocations(), CVDBGraphSeqIterator::GetAnnot(), SSeqTableContent::GetAnnot(), GetBioseqWithFootprintForNthRow(), CLDS2_DataLoader::GetChunk(), CCSraRefSeqIterator::GetCoverageAnnot(), CSNPDbSeqIterator::GetCoverageAnnot(), CSNPDbSeqIterator::GetFeatAnnot(), GetMasterBioseqWithFootprintOld(), CSNPDbSeqIterator::GetOverviewAnnot(), CSNPDbSeqIterator::GetPackedFeatAnnot(), CSraRun::GetSpotEntry(), CAlignGroup::GroupByLikeTaxIds(), CAlignGroup::GroupBySeqIds(), CAlignGroup::GroupBySequenceType(), CAlignGroup::GroupByStrand(), CAlignGroup::GroupByTaxIds(), CBamRefSeqInfo::LoadAlignChunk(), CFastaObjectLoader::LoadAlignsFromStream(), CMultiReader::LoadAnnot(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CFastaObjectLoader::LoadFromStream(), CTextAlignObjectLoader::LoadFromStream(), CAsnObjectLoader::LoadFromStream(), CBamRefSeqInfo::LoadPileupChunk(), CSeqAnnotFromFasta::MakeAsIsSeqAnnot(), CMakeCdrProds::MakeCdrProds(), COrf::MakeCDSAnnot(), MakeCompartment(), MakeEntryForDeltaConversion(), CBamIndex::MakeEstimatedCoverageAnnot(), CWig2tableApplication::MakeGraphAnnot(), CSeqAnnotFromFasta::MakeIBMSeqAnnot(), CBam2Seq_graph::MakeSeq_annot(), CBlobSplitterImpl::MakeSeq_annot(), CCSraRefSeqIterator::MakeSeq_annot(), CSeqAnnotFromFasta::MakeSeqAnnotFromFasta(), CWig2tableApplication::MakeTableAnnot(), CSeq_loc_Mapper_Base::Map(), CCdsToMatPeptide::MergeConvert(), CAnalyzeShiftApp::ProcessHGVS(), CAlignProjectItemExtension::ProjectItemAttached(), PromoteCDSToNucProtSet(), CGlimmerReader::Read(), CGFFReader::Read(), CUCSCRegionReader::ReadSeqAnnot(), CMicroArrayReader::ReadSeqAnnot(), CHgvsReader::ReadSeqAnnot(), CVcfReader::ReadSeqAnnot(), CRepeatMaskerReader::ReadSeqAnnot(), CFeature_table_reader_imp::ReadSequinFeatureTable(), AlignmentManager::RefineAlignment(), CDUpdater::reformatBioseq(), CTableAnnotDataSource::RemoveSeqLocs(), CAnnotationASN1::CImplementationData::ResetASN1(), CGtfExportJob::Run(), CLocalFinderApp::Run(), CGffExportJob::Run(), CDemoContigAssemblyApp::Run(), CTestCompartApplication::Run(), s_AddSitesToAnnot(), s_Align2Annot(), s_AlignSet2Annot(), s_DivvyUpAlignments_ProcessAnnot(), s_GetMappedFeat(), s_MakeNewMasterSeq(), UpdateViewer::SaveAlignments(), SetDenDiagSet(), CReadBlastApp::StoreBlast(), CMytestApplication::TestFeatureGeneOverlap(), TestOneGapSeq(), CPhrap_Contig::x_AddBaseSegFeats(), SWGSCreateInfo::x_AddFeatures(), CFastaReader::x_AddMultiwayAlignment(), CFastaReader::x_AddPairwiseAlignments(), CPromote::x_AddProtFeature(), CPhrap_Read::x_AddQualityFeat(), CPhrap_Contig::x_AddReadLocFeats(), CPhrap_Read::x_AddTagFeats(), CPhrap_Contig::x_AddTagFeats(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CAutogeneratedCleanup::x_BasicCleanupBioseq_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_data_annots_E_E(), CFeatureGenerator::SImplementation::x_CopyAdditionalFeatures(), CPromote::x_CopyCdregionToRNA(), CPhrap_Contig::x_CreateAlignAll(), CPhrap_Contig::x_CreateAlignOptimized(), CPhrap_Contig::x_CreateAlignPairs(), CGFFReader::x_CreateGeneFeatures(), CFeature_table_reader_imp::x_CreateGenesFromCDSs(), CPhrap_Contig::x_CreateGraph(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CProSplignJob::x_CreateOneProjectItem(), CNGAlignJob::x_CreateProjectItems(), CBLASTSeqToolJob::x_CreateProjectItems(), CMSAToolJob::x_CreateProjectItems(), CGroupAlignmentsJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFindOverlapJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CGBankLoadingJob::x_CreateProjectItems(), CCpgSearchJob::x_DoSearch(), CAppHitFilter::x_DumpOutput(), CSequenceUpdater::x_FuseProtFeatsForCDS(), CGvfReader::x_GetAnnotById(), CCreateGeneModelTask::x_GetCommand(), CCSraAlignIterator::x_GetMatchAnnot(), CBamAlignIterator::x_GetMatchEntry(), CWGSSeqIterator::x_GetQualityAnnot(), CCSraAlignIterator::x_GetQualityGraphAnnot(), CCSraShortReadIterator::x_GetQualityGraphAnnot(), CCSraRefSeqIterator::x_GetSeq_annot(), CBamAlignIterator::x_GetSeq_annot(), CCSraShortReadIterator::x_GetSeq_annot(), CSequenceUpdater::x_GetSeqAnnot_WithoutCDS(), CCreateGeneModelTask::x_Group_By_GeneID(), CIdMapperTestApp::x_HandleFeatures(), CGff2Reader::x_InitAnnot(), CMultiAlignView::x_MergeObjects(), CGvfReader::x_MergeRecord(), CGFFReader::x_PlaceAlignment(), CGFFReader::x_PlaceFeature(), CGff2Reader::x_ProcessAlignmentsGff(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CPromote::x_PromoteFeatures(), CNewCleanup_imp::x_RemoveEmptyFeatures(), CVariationNormalization_base< T >::x_Shift(), CGff2Reader::x_UpdateAnnotAlignment(), CModifySeqId::x_UpdateSeqAnnot(), CGff3Reader::xAddFeatureToAnnot(), CGff2Reader::xAddFeatureToAnnot(), CBedReader::xAppendFeatureBlock(), CBedReader::xAppendFeatureCds(), CBedReader::xAppendFeatureChrom(), CBedReader::xAppendFeatureGene(), CBedReader::xAppendFeatureRna(), CBedReader::xAppendFeatureThick(), CWiggleReader::xDumpChromValues(), CGff2Reader::xGenerateParentChildXrefs(), CWiggleReader::xGetAnnot(), CWiggleReader::xMakeGraphAnnot(), CWiggleReader::xMakeTableAnnot(), CUCSCRegionReader::xParseFeature(), CMicroArrayReader::xParseFeature(), CBedReader::xParseFeatureUserFormat(), and CVcfReader::xProcessDataLine().

CSeq_annot_Base::TData & CSeq_annot_Base::SetData ( void  )
inline

Assign a value to Data data member.

Returns
Reference to the data value.

Definition at line 863 of file Seq_annot_.hpp.

References m_Data, and ResetData().

void CSeq_annot_Base::SetDb ( CSeq_annot_Base::TDb  value)
inline

Assign a value to Db data member.

Parameters
valueValue to assign

Definition at line 762 of file Seq_annot_.hpp.

References m_Db, m_set_State, and value.

Referenced by CBlobSplitterImpl::MakeSeq_annot().

CSeq_annot_Base::TDb & CSeq_annot_Base::SetDb ( void  )
inline

Assign a value to Db data member.

Returns
Reference to the data value.

Definition at line 769 of file Seq_annot_.hpp.

References IsSetDb(), m_Db, m_set_State, and CSerialObject::UnassignedByte().

void CSeq_annot_Base::SetDesc ( CSeq_annot_Base::TDesc value)

Assign a value to Desc data member.

Parameters
valueReference to value.

Definition at line 222 of file Seq_annot_.cpp.

References m_Desc.

Referenced by CGBDocument::AddItems(), CAutogeneratedCleanup::BasicCleanupSeqAnnot(), BOOST_AUTO_TEST_CASE(), CTableImportDataSource::ConvertToSeqAnnot(), CTableAnnotDataSource::CreateSnps(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqAnnot(), FormatAsAsn(), CVDBGraphSeqIterator::GetAnnot(), CFindRSites::GetAnnot(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CBamRefSeqInfo::LoadPileupChunk(), CWig2tableApplication::MakeAnnot(), MakeCompartment(), CCSraAlignIterator::MakeEmptyMatchAnnot(), CBam2Seq_graph::MakeSeq_annot(), CBlobSplitterImpl::MakeSeq_annot(), CCSraRefSeqIterator::MakeSeq_annot(), CUCSCRegionReader::ReadSeqAnnot(), CMicroArrayReader::ReadSeqAnnot(), CBedReader::ReadSeqAnnot(), CFeature_table_reader_imp::ReadSequinFeatureTable(), CAnnotationASN1::CImplementationData::ResetASN1(), CDemoContigAssemblyApp::Run(), CAnnotConfigUtils::SetConfigObject(), CReadBlastApp::StoreBlast(), sx_SetTitle(), sx_SetZoomLevel(), CTrackData::WriteToAnnot(), CBedReader::x_AppendAnnot(), CAutogeneratedCleanup::x_BasicCleanupBioseq_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_annot_E_E(), CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_data_annots_E_E(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CGBankLoadingJob::x_CreateProjectItems(), CGvfReader::x_GetAnnotById(), CTableAnnotDataSource::x_GetColumnMetaInfo(), CCSraAlignIterator::x_GetEmptyMatchAnnot(), CWGSSeqIterator::x_GetQualityAnnot(), CCSraRefSeqIterator::x_GetSeq_annot(), CBamAlignIterator::x_GetSeq_annot(), CCSraShortReadIterator::x_GetSeq_annot(), CGff2Reader::x_InitAnnot(), CGff2Reader::x_ProcessAlignmentsGff(), CReaderBase::xAddConversionInfo(), CBedReader::xAssignBedColumnCount(), CVcfReader::xAssignVcfMeta(), CReaderBase::xParseBrowserLine(), and CGvfReader::xPostProcessAnnot().

CSeq_annot_Base::TDesc & CSeq_annot_Base::SetDesc ( void  )

Assign a value to Desc data member.

Returns
Reference to the data value.

Definition at line 227 of file Seq_annot_.cpp.

References m_Desc.

Referenced by CSeq_annot::AddComment(), CSeq_annot::AddUserObject(), CSeq_annot::SetCreateDate(), CSeq_annot::SetNameDesc(), CSeq_annot::SetTitleDesc(), and CSeq_annot::SetUpdateDate().

CSeq_annot_Base::TId & CSeq_annot_Base::SetId ( void  )
inline

Assign a value to Id data member.

Returns
Reference to the data value.

Definition at line 727 of file Seq_annot_.hpp.

References m_Id, and m_set_State.

Referenced by CAnnotationASN1::CImplementationData::DumpEvidence(), CBlobSplitterImpl::MakeSeq_annot(), CGvfReader::x_GetAnnotById(), and CGff2Reader::xAssignAnnotId().

void CSeq_annot_Base::SetName ( const TName value)
inline
CSeq_annot_Base::TName & CSeq_annot_Base::SetName ( void  )
inline

Assign a value to Name data member.

Returns
Reference to the data value.

Definition at line 809 of file Seq_annot_.hpp.

References IsSetName(), m_Name, m_set_State, and CSerialObject::UnassignedString().

Member Data Documentation

CRef< TData > CSeq_annot_Base::m_Data
private

Definition at line 561 of file Seq_annot_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), GetData(), IsSetData(), ResetData(), and SetData().

int CSeq_annot_Base::m_Db
private

Definition at line 558 of file Seq_annot_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), GetDb(), ResetDb(), and SetDb().

CRef< TDesc > CSeq_annot_Base::m_Desc
private

Definition at line 560 of file Seq_annot_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), GetDesc(), IsSetDesc(), ResetDesc(), and SetDesc().

list< CRef< CAnnot_id > > CSeq_annot_Base::m_Id
private

Definition at line 557 of file Seq_annot_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), GetId(), ResetId(), and SetId().

string CSeq_annot_Base::m_Name
private

Definition at line 559 of file Seq_annot_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), GetName(), ResetName(), and SetName().

Uint4 CSeq_annot_Base::m_set_State[1]
private

The documentation for this class was generated from the following files:
Modified on Tue Jul 25 19:57:05 2017 by modify_doxy.py rev. 533848