Search Toolkit Book for CSeq_entry
#include <objects/seqset/Seq_entry.hpp>
Inheritance diagram for CSeq_entry:
Collaboration diagram for CSeq_entry:
Public Types | |
| enum | ELabelType { eType , eContent , eBoth } |
| typedef list< CRef< CSeq_annot > > | TAnnot |
| Public Types inherited from CSeq_entry_Base | |
| enum | E_Choice { e_not_set = 0 , e_Seq , e_Set } |
| Choice variants. More... | |
| enum | E_ChoiceStopper { e_MaxChoice = 3 } |
| Maximum+1 value of the choice variant enumerator. More... | |
| typedef CBioseq | TSeq |
| typedef CBioseq_set | TSet |
| 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... | |
Public Member Functions | |
| CSeq_entry (void) | |
| ~CSeq_entry (void) | |
| void | Parentize (void) |
| void | ParentizeOneLevel (void) |
| void | ResetParentEntry (void) |
| void | SetParentEntry (CSeq_entry *entry) |
| CSeq_entry * | GetParentEntry (void) const |
| bool | IsSetDescr (void) const |
| const CSeq_descr & | GetDescr (void) const |
| void | SetDescr (CSeq_descr &value) |
| CSeq_descr & | SetDescr (void) |
| bool | IsSetAnnot (void) const |
| const TAnnot & | GetAnnot (void) const |
| TAnnot & | SetAnnot (void) |
| void | GetLabel (string *label, ELabelType type) const |
| void | ReassignConflictingIds (void) |
| Public Member Functions inherited from CSeq_entry_Base | |
| CSeq_entry_Base (void) | |
| virtual | ~CSeq_entry_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| virtual void | Reset (void) |
| Reset the whole object. More... | |
| virtual void | ResetSelection (void) |
| Reset the selection (set it to e_not_set). More... | |
| E_Choice | Which (void) const |
| Which variant is currently selected. More... | |
| void | CheckSelected (E_Choice index) const |
| Verify selection, throw exception if it differs from the expected. More... | |
| void | ThrowInvalidSelection (E_Choice index) const |
| Throw 'InvalidSelection' exception. More... | |
| void | Select (E_Choice index, EResetVariant reset=eDoResetVariant) |
| Select the requested variant if needed. More... | |
| void | Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool) |
| Select the requested variant if needed, allocating CObject variants from memory pool. More... | |
| bool | IsSeq (void) const |
| Check if variant Seq is selected. More... | |
| const TSeq & | GetSeq (void) const |
| Get the variant data. More... | |
| TSeq & | SetSeq (void) |
| Select the variant. More... | |
| void | SetSeq (TSeq &value) |
| Select the variant and set its data. More... | |
| bool | IsSet (void) const |
| Check if variant Set is selected. More... | |
| const TSet & | GetSet (void) const |
| Get the variant data. More... | |
| TSet & | SetSet (void) |
| Select the variant. More... | |
| void | SetSet (TSet &value) |
| Select the variant and set its data. 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 |
| Public Member Functions inherited from CSerialUserOp | |
| virtual | ~CSerialUserOp () |
Protected Member Functions | |
| virtual void | UserOp_Assign (const CSerialUserOp &source) |
| Will be called after copying the datatool-generated members. More... | |
| virtual bool | UserOp_Equals (const CSerialUserOp &object) const |
| Will be called after comparing the datatool-generated members. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Private Types | |
| typedef CSeq_entry_Base | Tparent |
Private Member Functions | |
| CSeq_entry (const CSeq_entry &value) | |
| CSeq_entry & | operator= (const CSeq_entry &value) |
Private Attributes | |
| CSeq_entry * | m_ParentEntry |
Additional Inherited Members | |
| Static Public Member Functions inherited from CSeq_entry_Base | |
| static string | SelectionName (E_Choice index) |
| Retrieve selection name (for diagnostic purposes). 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) |
| 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... | |
Detailed Description
Definition at line 55 of file Seq_entry.hpp.
Member Typedef Documentation
◆ TAnnot
| typedef list< CRef< CSeq_annot > > CSeq_entry::TAnnot |
Definition at line 86 of file Seq_entry.hpp.
◆ Tparent
|
private |
Definition at line 57 of file Seq_entry.hpp.
Member Enumeration Documentation
◆ ELabelType
| Enumerator | |
|---|---|
| eType | |
| eContent | |
| eBoth | |
Definition at line 91 of file Seq_entry.hpp.
Constructor & Destructor Documentation
◆ CSeq_entry() [1/2]
|
inline |
Definition at line 125 of file Seq_entry.hpp.
Referenced by CSraRun::GetSpotEntry().
◆ ~CSeq_entry()
| CSeq_entry::~CSeq_entry | ( | void | ) |
Definition at line 57 of file Seq_entry.cpp.
◆ CSeq_entry() [2/2]
|
private |
Member Function Documentation
◆ GetAnnot()
| const CSeq_entry::TAnnot & CSeq_entry::GetAnnot | ( | void | ) | const |
Definition at line 179 of file Seq_entry.cpp.
References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), NCBI_THROW, CSeq_entry_Base::SelectionName(), and CSeq_entry_Base::Which().
Referenced by BOOST_AUTO_TEST_CASE(), CValidError_imp::GatherTentativeName(), GetAlignmentFromStream(), CMultiReader::LoadIndexedAnnot(), CBamRefSeqInfo::LoadMainChunk(), CBamRefSeqInfo::LoadMainEntry(), CBam2GraphApp::ProcessFile(), ReadMsa(), CCdsToMatPeptide::RemoveFeature(), and CFeatureTableReader::xCheckIfNeedConversion().
◆ GetDescr()
| const CSeq_descr & CSeq_entry::GetDescr | ( | void | ) | const |
Definition at line 120 of file Seq_entry.cpp.
References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), NCBI_THROW, CSeq_entry_Base::SelectionName(), and CSeq_entry_Base::Which().
Referenced by seqsubmit_split::CSeqEntryHelper::BuildObject(), CWithdrawSequences::CopyDescrToEntry(), CValidError_imp::GatherTentativeName(), CBioseq::GetClosestDescriptor(), GetSourceDescriptors(), MoveBiomolToTop(), s_GetSourceDescriptors(), s_GetTaxId(), s_IsDescOnSeqEntry(), CCleanupHugeAsnReader::x_AddTopLevelDescriptors(), CPrimeCacheApplication::x_Process_Fasta(), CBsDiffApp::xGetBioSampleAccs(), CBsDiffApp::xGetBioSource(), and seqsubmit_split::CSeqSubSplitter::xTryProcessSeqEntry().
◆ GetLabel()
| void CSeq_entry::GetLabel | ( | string * | label, |
| ELabelType | type | ||
| ) | const |
Definition at line 274 of file Seq_entry.cpp.
References CSeq_entry_Base::e_not_set, CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CBioseq_set::GetLabel(), CBioseq::GetLabel(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), label, s_GetBioseqLabelType(), s_GetBioseqSetLabelType(), and CSeq_entry_Base::Which().
Referenced by CGBProjectHelper::AddProjectItemsFromRID(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CCleanupApp::HandleSeqEntry(), CValidError_imp::PostErr(), and s_Process().
◆ GetParentEntry()
|
inline |
Definition at line 131 of file Seq_entry.hpp.
References m_ParentEntry.
Referenced by CTable2AsnContext::ApplyCreateUpdateDates(), Convert_Bioseq_Seq_entry(), sequpd::FixCollidingIDs_Bioseq(), get_parent_seqset(), CValidError_imp::GetAncestor(), CBioseq::GetClosestDescriptor(), CBioseq::GetParentSet(), CBioseq_set::GetParentSet(), CTable2AsnContext::MergeWithTemplate(), s_GetTaxId(), sx_ComesBefore(), sx_FindBestId(), sx_GetParentLevel(), sx_Level(), CDeflineProcess::UnindexedProcess(), CValidError_bioseq::ValidateSeqParts(), and CFeatureTableReader::xCheckIfNeedConversion().
◆ IsSetAnnot()
| bool CSeq_entry::IsSetAnnot | ( | void | ) | const |
Definition at line 165 of file Seq_entry.cpp.
References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), and CSeq_entry_Base::Which().
Referenced by subfuse::CSubmissionCollector::AdjustLocalIds(), CValidError_imp::GatherTentativeName(), CMultiReader::LoadIndexedAnnot(), and CFeatureTableReader::xCheckIfNeedConversion().
◆ IsSetDescr()
| bool CSeq_entry::IsSetDescr | ( | void | ) | const |
Definition at line 106 of file Seq_entry.cpp.
References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), and CSeq_entry_Base::Which().
Referenced by seqsubmit_split::CSeqEntryHelper::BuildObject(), CWithdrawSequences::CopyDescrToEntry(), CValidError_imp::GatherTentativeName(), CBioseq::GetClosestDescriptor(), GetSourceDescriptors(), MoveBiomolToTop(), CRemoteUpdater::PostProcessPubs(), CCleanup::RemoveNcbiCleanupObject(), s_GetSourceDescriptors(), s_GetTaxId(), s_IsDescOnSeqEntry(), SetTitle(), SortSeqDescr(), CCleanupHugeAsnReader::x_AddTopLevelDescriptors(), CNewCleanup_imp::x_CopyGBBlockDivToOrgnameDiv(), CNewCleanup_imp::x_MoveNpDBlinks(), CPrimeCacheApplication::x_Process_Fasta(), CNewCleanup_imp::x_RemoveDupBioSource(), CNewCleanup_imp::x_SortSeqDescs(), seqsubmit_split::CSeqSubSplitter::xTryProcessSeqEntry(), and CRemoteUpdater::xUpdatePubReferences().
◆ operator=()
|
private |
◆ Parentize()
| void CSeq_entry::Parentize | ( | void | ) |
Definition at line 71 of file Seq_entry.cpp.
References CSeq_entry_Base::e_not_set, CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, NON_CONST_ITERATE, CBioseq::SetParentEntry(), CBioseq_set::SetParentEntry(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), si, and CSeq_entry_Base::Which().
Referenced by BOOST_AUTO_TEST_CASE(), CFeatureTableReader::ConvertNucSetToSet(), CSeqEntryGetSource::CSeqEntryGetSource(), CSeqEntrySource::CSeqEntrySource(), CDumpASNIndex::DumpBlob(), CNewCleanup_imp::EnteringEntry(), CPrimeCacheApplication::CCacheBioseq::operator()(), CTbl2AsnApp::ProcessAlignmentFile(), CTbl2AsnApp::ProcessOneEntry(), CTbl2AsnApp::ProcessSingleEntry(), CFastaReader::ReadAlignedSet(), CFastaReaderEx::ReadDeltaFasta(), ReadEntry(), CFastaReader::ReadOneSeq(), CFastaReader::ReadSet(), ReassignConflictingIds(), CReadBlastApp::Run(), CTSE_Info::SetSeq_entry(), CUpdateSeq_Input::x_AddNewEntryToScope(), CPrimeCacheApplication::x_CacheSeqEntry(), CSeqMasterIndex::x_Initialize(), CPrimeCacheApplication::x_Process_Fasta(), CMultiReader::xApplyTemplate(), and CFeatureTableReader::xConvertSeqIntoSeqSet().
◆ ParentizeOneLevel()
| void CSeq_entry::ParentizeOneLevel | ( | void | ) |
Definition at line 89 of file Seq_entry.cpp.
References CSeq_entry_Base::e_not_set, CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, NON_CONST_ITERATE, CBioseq::SetParentEntry(), CBioseq_set::SetParentEntry(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), si, and CSeq_entry_Base::Which().
Referenced by CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), UserOp_Assign(), CBioseq_Info::x_ParentAttach(), and CBioseq_set_Info::x_ParentAttach().
◆ ReassignConflictingIds()
| void CSeq_entry::ReassignConflictingIds | ( | void | ) |
Definition at line 548 of file Seq_entry.cpp.
References ConstBegin(), ConstRef(), map_checker< Container >::end(), eUnknown, map_checker< Container >::find(), CSeq_id_Handle::GetGiHandle(), CSeq_id_Handle::GetHandle(), GI_CONST, ITERATE, NCBI_THROW_FMT, NON_CONST_ITERATE, Parentize(), SerialClone(), sx_AddId(), sx_CanReassign(), sx_MakeUniqueId(), and sx_ProcessId().
Referenced by BOOST_AUTO_TEST_CASE(), HandleCollidingIds(), CCatenatedPresenter::Run(), TestCollidingAccessionFixes(), and CUpdateSeq_Input::x_FixCollidingIDs_Entry().
◆ ResetParentEntry()
| void CSeq_entry::ResetParentEntry | ( | void | ) |
Definition at line 61 of file Seq_entry.cpp.
References m_ParentEntry.
Referenced by CMultiReader::xApplyTemplate().
◆ SetAnnot()
| CSeq_entry::TAnnot & CSeq_entry::SetAnnot | ( | void | ) |
Definition at line 195 of file Seq_entry.cpp.
References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, NCBI_THROW, CSeq_entry_Base::SelectionName(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), and CSeq_entry_Base::Which().
Referenced by subfuse::CSubmissionCollector::AdjustLocalIds(), CCdsToMatPeptide::FindAnnot(), sequpd::FixCollidingIDs_Bioseq(), CGeneModelTrack::GenerateAsn1(), CCDDDataLoader_Impl::GetBlobBySeq_ids(), CCdsToMatPeptide::RemoveFeature(), SetProteinPartial(), CGC_Assembly_Parser::x_CopyData(), CBamAlignIterator::x_GetMatchEntry(), CBamRefSeqInfo::x_LoadRangesEstimated(), CGC_Assembly_Parser::x_ParseGCSequence(), and CPSGS_CDDProcessor::x_SendAnnot().
◆ SetDescr() [1/2]
| void CSeq_entry::SetDescr | ( | CSeq_descr & | value | ) |
Definition at line 134 of file Seq_entry.cpp.
References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, NCBI_THROW, CSeq_entry_Base::SelectionName(), CBioseq_Base::SetDescr(), CBioseq_set_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), rapidjson::value, and CSeq_entry_Base::Which().
Referenced by AddOrgmodDescriptor(), AddStrainDescriptor(), AddStrainDescriptorNew(), CTable2AsnContext::ApplyCreateUpdateDates(), CMultiReader::ApplyDescriptors(), CTable2AsnContext::ApplyFileTracks(), CTable2AsnContext::ApplyUpdateDate(), BOOST_AUTO_TEST_CASE(), BuildGoodSegSet(), seqsubmit_split::CSeqEntryHelper::BuildObject(), CWithdrawSequences::CopyDescrToEntry(), g_ApplyDescriptors(), CTable2AsnContext::MergeSeqDescr(), MoveBiomolToTop(), CCleanup::RemoveNcbiCleanupObject(), SetTitle(), SortSeqDescr(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CCleanupHugeAsnReader::x_AddTopLevelDescriptors(), CGC_Assembly_Parser::x_CopyData(), CNewCleanup_imp::x_CopyGBBlockDivToOrgnameDiv(), CNewCleanup_imp::x_MoveNpDBlinks(), CGC_Assembly_Parser::x_ParseGCSequence(), CSequenceUpdater::x_RemoveDescriptorsFromImportedProducts(), CNewCleanup_imp::x_RemoveDupBioSource(), CNewCleanup_imp::x_SortSeqDescs(), CFeatureTableReader::xAddProteinToSeqEntry(), seqsubmit_split::CSeqSubSplitter::xTryProcessSeqEntry(), and CRemoteUpdater::xUpdatePubReferences().
◆ SetDescr() [2/2]
| CSeq_descr & CSeq_entry::SetDescr | ( | void | ) |
Definition at line 150 of file Seq_entry.cpp.
References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, NCBI_THROW, CSeq_entry_Base::SelectionName(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), and CSeq_entry_Base::Which().
◆ SetParentEntry()
| void CSeq_entry::SetParentEntry | ( | CSeq_entry * | entry | ) |
Definition at line 66 of file Seq_entry.cpp.
References m_ParentEntry.
◆ UserOp_Assign()
|
protectedvirtual |
Will be called after copying the datatool-generated members.
Implements CSerialUserOp.
Definition at line 238 of file Seq_entry.cpp.
References m_ParentEntry, and ParentizeOneLevel().
◆ UserOp_Equals()
|
protectedvirtual |
Will be called after comparing the datatool-generated members.
Implements CSerialUserOp.
Definition at line 244 of file Seq_entry.cpp.
Member Data Documentation
◆ m_ParentEntry
|
private |
Definition at line 117 of file Seq_entry.hpp.
Referenced by GetParentEntry(), ResetParentEntry(), SetParentEntry(), and UserOp_Assign().
The documentation for this class was generated from the following files:
- include/objects/seqset/Seq_entry.hpp
- src/objects/seqset/Seq_entry.cpp
