Search Toolkit Book for CSeq_annot
#include <objects/seq/Seq_annot.hpp>
Inheritance diagram for CSeq_annot:
Collaboration diagram for CSeq_annot:
Public Member Functions | |
| CSeq_annot (void) | |
| ~CSeq_annot (void) | |
| void | AddName (const string &name) |
| void | SetNameDesc (const string &name) |
| void | SetTitleDesc (const string &title) |
| void | AddTitle (const string &title) |
| void | SetTitle (const string &title) |
| void | AddComment (const string &comment) |
| void | SetCreateDate (const CTime &dt) |
| void | SetCreateDate (CDate &dt) |
| void | SetUpdateDate (const CTime &dt) |
| void | SetUpdateDate (CDate &dt) |
| void | AddUserObject (CUser_object &obj) |
| bool | IsFtable (void) const |
| bool | IsAlign (void) const |
| bool | IsGraph (void) const |
| bool | IsIds (void) const |
| bool | IsLocs (void) const |
| bool | IsSeq_table (void) const |
| Public Member Functions inherited from CSeq_annot_Base | |
| 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 TId & | GetId (void) const |
| Get the Id member data. More... | |
| TId & | SetId (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... | |
| TDb & | SetDb (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 TName & | GetName (void) const |
| Get the Name member data. More... | |
| void | SetName (const TName &value) |
| Assign a value to Name data member. More... | |
| void | SetName (TName &&value) |
| TName & | SetName (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 TDesc & | GetDesc (void) const |
| Get the Desc member data. More... | |
| void | SetDesc (TDesc &value) |
| Assign a value to Desc data member. More... | |
| TDesc & | SetDesc (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 TData & | GetData (void) const |
| Get the Data member data. More... | |
| void | SetData (TData &value) |
| Assign a value to Data data member. More... | |
| TData & | SetData (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 CTypeInfo * | GetThisTypeInfo (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 string & | GetNamespaceName (void) const |
| Get namespace name. More... | |
| bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More... | |
| const string & | GetNamespacePrefix (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... | |
| CObject & | operator= (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 bool | ExtractZoomLevel (const string &full_name, string *acc_ptr, int *zoom_level_ptr) |
| Extract optional zoom level suffix from named annotation string. More... | |
| static string | CombineWithZoomLevel (const string &acc, int zoom_level) |
| Combine accession string and zoom level into a string with separator. More... | |
| static void | AddZoomLevel (string &acc, int zoom_level) |
| Static Public Member Functions inherited from CSeq_annot_Base | |
| 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_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) |
Private Types | |
| typedef CSeq_annot_Base | Tparent |
Private Member Functions | |
| CSeq_annot (const CSeq_annot &value) | |
| CSeq_annot & | operator= (const CSeq_annot &value) |
Additional Inherited Members | |
| Public Types inherited from CSeq_annot_Base | |
| 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... | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_id , e_db , e_name , e_desc , e_data } |
| typedef list< CRef< CAnnot_id > > | TId |
| typedef int | TDb |
| typedef string | TName |
| typedef CAnnot_descr | TDesc |
| typedef C_Data | TData |
| typedef Tparent::CMemberIndex< E_memberIndex, 6 > | TmemberIndex |
| 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< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| 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
Definition at line 57 of file Seq_annot.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 59 of file Seq_annot.hpp.
Constructor & Destructor Documentation
◆ CSeq_annot() [1/2]
|
inline |
Definition at line 153 of file Seq_annot.hpp.
◆ ~CSeq_annot()
| CSeq_annot::~CSeq_annot | ( | void | ) |
Definition at line 56 of file Seq_annot.cpp.
◆ CSeq_annot() [2/2]
|
private |
Member Function Documentation
◆ AddComment()
Definition at line 113 of file Seq_annot.cpp.
References CAnnot_descr_Base::Set(), CAnnotdesc_Base::SetComment(), and CSeq_annot_Base::SetDesc().
Referenced by CCreateNeedlemanWunschJob::x_CreateProjectItems(), CCpgSearchJob::x_DoSearch(), and CAppHitFilter::x_DumpOutput().
◆ AddName()
Definition at line 61 of file Seq_annot.cpp.
References SetNameDesc().
◆ AddTitle()
Definition at line 90 of file Seq_annot.cpp.
References SetTitleDesc().
◆ AddUserObject()
| void CSeq_annot::AddUserObject | ( | CUser_object & | obj | ) |
Definition at line 169 of file Seq_annot.cpp.
References CAnnot_descr_Base::Set(), CSeq_annot_Base::SetDesc(), and CAnnotdesc_Base::SetUser().
Referenced by CTableImportDataSource::ConvertToSeqAnnot(), CBlastFormatUtil::CreateSeqAnnotFromSeqAlignSet(), and CBamUtils::UpdateCoverageGraphInfo().
◆ AddZoomLevel()
Definition at line 262 of file Seq_annot.cpp.
References ExtractZoomLevel(), NStr::IntToString(), NCBI_ANNOT_TRACK_ZOOM_LEVEL_SUFFIX, and NCBI_THROW_FMT.
Referenced by AddZoomLevel(), and CombineWithZoomLevel().
◆ CombineWithZoomLevel()
Combine accession string and zoom level into a string with separator.
If the argument string already contains zoom level verify it's the same as the zoom_level argument. Zoom level value of -1 can be used to add wildcard @*.
Definition at line 254 of file Seq_annot.cpp.
References AddZoomLevel().
Referenced by CombineWithZoomLevel(), CSNPClient::GetAnnotInfo(), and sx_CombineWithZoomLevel().
◆ ExtractZoomLevel()
|
static |
Extract optional zoom level suffix from named annotation string.
returns true if zoom level explicitly defined in the full_name argument. The accession string without zoom level will be written by acc_ptr pointer if it's not null. Zoom level will be written by zoom_level_ptr pointer if it's not null. Absent zoom level will be represented by value 0. Wildcard zoom level will be represented by value -1.
Definition at line 215 of file Seq_annot.cpp.
References NCBI_ANNOT_TRACK_ZOOM_LEVEL_SUFFIX, NCBI_ANNOT_TRACK_ZOOM_LEVEL_SUFFIX_LEN, NPOS, and NStr::StringToInt().
Referenced by AddZoomLevel(), and ExtractZoomLevel().
◆ IsAlign()
| bool CSeq_annot::IsAlign | ( | void | ) | const |
Definition at line 182 of file Seq_annot.cpp.
References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsAlign(), and CSeq_annot_Base::IsSetData().
Referenced by CTableDataSeq_annot::CreateObject(), CTableDataAlnSummary::CTableDataAlnSummary(), CMAViewManager::DoTransition(), CAlnSummaryViewFactory::IsCompatibleWith(), CMultiAlignViewFactory::IsCompatibleWith(), CMAViewManager::NeedAnchorPanel(), CValidError_annot::ValidateSeqAnnot(), CAlnWriter::WriteAnnot(), CPslWriter::WriteAnnot(), CUpdateMultiSeq_Dlg::x_CreateAlignmentForIdenticalUpdates(), CBLASTSeqToolJob::x_CreateProjectItems(), CUpdateMultiSeq_Dlg::x_GenerateAlignments(), CGff2Writer::x_WriteSeqAnnotHandle(), and CGff3Writer::x_WriteSeqAnnotHandle().
◆ IsFtable()
| bool CSeq_annot::IsFtable | ( | void | ) | const |
Definition at line 177 of file Seq_annot.cpp.
References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsFtable(), and CSeq_annot_Base::IsSetData().
Referenced by CImportFeatTable::AddSeqAnnotToSeqEntry(), subfuse::CSubmissionCollector::AdjustLocalIds(), CDiscrepancyContext::AutofixSeq_annot(), ChangeId(), ChangeProductId(), FeatUtil::ContainsData(), CTableDataSeq_annot::CreateObject(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqAnnot(), CAnnotationASN1::ExtractModels(), CTableDataFTable::Init(), CFeatTableViewFactory::IsCompatibleWith(), CWriteUtil::IsThreeFeatFormat(), s_IsMergeableFeatureTable(), s_ReadMultipleTablesFromString(), s_ReadOneTableFromString(), s_RemoveOrgFromEndOfProtein(), s_UpdateFeatureIds(), CNewCleanup_imp::ShouldRemoveAnnot(), CValidError_annot::ValidateSeqAnnot(), CValidError_annot::ValidateSeqAnnotContext(), CSequenceUpdater::x_AdjustProteinFeature(), CImportFeatTable::x_CheckCollidingIds(), CImportFeatTable::x_CheckConsistentProteinIds(), CImportFeatTable::x_ContainsDuplicateIds(), CImportFeatTable::x_CreateCommand(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CAlignFilter::x_GetRegionMap(), CNewCleanup_imp::x_RemoveEmptyFeatures(), CSequenceUpdater::x_UpdateProteinID(), CGff2Reader::xGenerateParentChildXrefs(), CFeatureTableReader::xParseCdregions(), CMultiReaderApp::xProcess5ColFeatTable(), CMultiReaderApp::xProcessRmo(), and CBedGraphWriter::xWriteAnnotFeatureTable().
◆ IsGraph()
| bool CSeq_annot::IsGraph | ( | void | ) | const |
Definition at line 187 of file Seq_annot.cpp.
References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsGraph(), and CSeq_annot_Base::IsSetData().
Referenced by CBamUtils::GetCoverageGraphInfo(), s_LoadSeqAnnot(), CBamUtils::UpdateCoverageGraphInfo(), CValidError_annot::ValidateSeqAnnot(), CValidError_annot::ValidateSeqAnnotContext(), CWiggleWriter::WriteAnnot(), and CBedGraphWriter::xWriteAnnotGraphs().
◆ IsIds()
| bool CSeq_annot::IsIds | ( | void | ) | const |
Definition at line 192 of file Seq_annot.cpp.
References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsIds(), and CSeq_annot_Base::IsSetData().
Referenced by CValidError_annot::ValidateSeqAnnot().
◆ IsLocs()
| bool CSeq_annot::IsLocs | ( | void | ) | const |
Definition at line 197 of file Seq_annot.cpp.
References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsLocs(), and CSeq_annot_Base::IsSetData().
Referenced by CValidError_annot::ValidateSeqAnnot().
◆ IsSeq_table()
| bool CSeq_annot::IsSeq_table | ( | void | ) | const |
Definition at line 202 of file Seq_annot.cpp.
References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsSeq_table(), and CSeq_annot_Base::IsSetData().
Referenced by CTableDataSeq_annot::CreateObject(), CDataTrackUtils::GetColumnHeader(), s_GetAnnotId(), CWiggleWriter::WriteAnnot(), and CBedGraphWriter::xWriteAnnotSeqTable().
◆ operator=()
|
private |
◆ SetCreateDate() [1/2]
| void CSeq_annot::SetCreateDate | ( | CDate & | dt | ) |
Definition at line 128 of file Seq_annot.cpp.
References CAnnot_descr_Base::Set(), CAnnotdesc_Base::SetCreate_date(), and CSeq_annot_Base::SetDesc().
◆ SetCreateDate() [2/2]
Definition at line 121 of file Seq_annot.cpp.
Referenced by CGBProjectHelper::AddProjectItemsFromRID(), CEntrezDB::CreateAnnot_Nuc_Prot(), CFindRSites::GetAnnot(), CProSplignJob::x_CreateOneProjectItem(), CBLASTSeqToolJob::x_CreateProjectItems(), CGroupAlignmentsJob::x_CreateProjectItems(), CMSAToolJob::x_CreateProjectItems(), CNGAlignJob::x_CreateProjectItems(), CAdvancedCleanupJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFindOverlapJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CCpgSearchJob::x_DoSearch(), and CCreateGeneModelTask::x_GetCommand().
◆ SetNameDesc()
Definition at line 66 of file Seq_annot.cpp.
References CAnnot_descr_Base::Set(), CSeq_annot_Base::SetDesc(), and CAnnotdesc_Base::SetName().
Referenced by AddName(), CGBProjectHelper::AddProjectItemsFromRID(), CAttachedHandles::Attach(), CEntrezDB::CreateAnnot_Nuc_Prot(), CAddFeatChecker::Do(), CVcfObjectLoader::Execute(), CBedAnnotAssembler::FinalizeAnnot(), CFindRSites::GetAnnot(), SSeqTableConverter::GetAnnots(), CAsnObjectLoader::LoadFromStream(), CCSRAFileInfo::LoadReadsBlob(), NameAnnot(), CTestCompartApplication::Run(), CLocalFinderApp::Run(), CGeneModelDemoApp::Run(), s_CollapseProjectFolder(), sx_SetOverviewName(), sx_SetTitle(), CTrackData::WriteToAnnot(), CProSplignJob::x_CreateOneProjectItem(), CBLASTSeqToolJob::x_CreateProjectItems(), CGroupAlignmentsJob::x_CreateProjectItems(), CMSAToolJob::x_CreateProjectItems(), CNGAlignJob::x_CreateProjectItems(), CAdvancedCleanupJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFindOverlapJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CCpgSearchJob::x_DoSearch(), CCreateGeneModelTask::x_GetCommand(), CGBProjectTool::x_LoadGeneralData(), x_NewAnnot(), CGff2Reader::x_ProcessAlignmentsGff(), CReaderBase::xAssignTrackData(), CReaderBase::xCreateSeqAnnot(), CBedReader::xCreateSeqAnnot(), and CGff3Reader::xProcessAlignmentData().
◆ SetTitle()
Definition at line 84 of file Seq_annot.cpp.
References SetTitleDesc().
◆ SetTitleDesc()
Definition at line 96 of file Seq_annot.cpp.
References CAnnot_descr_Base::Set(), CSeq_annot_Base::SetDesc(), and CAnnotdesc_Base::SetTitle().
Referenced by AddTitle(), CTableImportDataSource::ConvertToSeqAnnot(), CBedAnnotAssembler::FinalizeAnnot(), CFindRSites::GetAnnot(), CAsnObjectLoader::LoadFromStream(), NameAnnot(), CTestCompartApplication::Run(), CGeneModelDemoApp::Run(), s_CollapseProjectFolder(), SetTitle(), CTrackData::WriteToAnnot(), CBLASTSeqToolJob::x_CreateProjectItems(), CNGAlignJob::x_CreateProjectItems(), CAdvancedCleanupJob::x_CreateProjectItems(), CCreateGeneModelTask::x_GetCommand(), CGff2Reader::x_ProcessAlignmentsGff(), CReaderBase::xAssignTrackData(), CReaderBase::xCreateSeqAnnot(), CBedReader::xCreateSeqAnnot(), and CGff3Reader::xProcessAlignmentData().
◆ SetUpdateDate() [1/2]
| void CSeq_annot::SetUpdateDate | ( | CDate & | dt | ) |
Definition at line 152 of file Seq_annot.cpp.
References CAnnot_descr_Base::Set(), CSeq_annot_Base::SetDesc(), and CAnnotdesc_Base::SetUpdate_date().
◆ SetUpdateDate() [2/2]
Definition at line 145 of file Seq_annot.cpp.
The documentation for this class was generated from the following files:
- include/objects/seq/Seq_annot.hpp
- src/objects/seq/Seq_annot.cpp
