NCBI C++ ToolKit
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Classes | |
class | CBioseq_set_Base |
*** Sequence Collections ******************************** * just a collection More... | |
class | CSeq_entry_Base |
CSeq_entry_Base –. More... | |
Typedefs | |
typedef CSerialObject | CBioseq_set_Base::Tparent |
typedef CObject_id | CBioseq_set_Base::TId |
typedef CDbtag | CBioseq_set_Base::TColl |
typedef int | CBioseq_set_Base::TLevel |
typedef EClass | CBioseq_set_Base::TClass |
typedef string | CBioseq_set_Base::TRelease |
typedef CDate | CBioseq_set_Base::TDate |
typedef CSeq_descr | CBioseq_set_Base::TDescr |
typedef list< CRef< CSeq_entry > > | CBioseq_set_Base::TSeq_set |
typedef list< CRef< CSeq_annot > > | CBioseq_set_Base::TAnnot |
typedef Tparent::CMemberIndex< E_memberIndex, 10 > | CBioseq_set_Base::TmemberIndex |
typedef CSerialObject | CSeq_entry_Base::Tparent |
typedef CBioseq | CSeq_entry_Base::TSeq |
typedef CBioseq_set | CSeq_entry_Base::TSet |
Functions | |
CBioseq_set_Base::CBioseq_set_Base (void) | |
virtual | CBioseq_set_Base::~CBioseq_set_Base (void) |
CBioseq_set_Base::DECLARE_INTERNAL_TYPE_INFO () | |
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | CBioseq_set_Base::EClass (void) |
Access to EClass's attributes (values, names) as defined in spec. More... | |
bool | CBioseq_set_Base::IsSetId (void) const |
Check if a value has been assigned to Id data member. More... | |
bool | CBioseq_set_Base::CanGetId (void) const |
Check if it is safe to call GetId method. More... | |
void | CBioseq_set_Base::ResetId (void) |
Reset Id data member. More... | |
const TId & | CBioseq_set_Base::GetId (void) const |
Get the Id member data. More... | |
void | CBioseq_set_Base::SetId (TId &value) |
Assign a value to Id data member. More... | |
TId & | CBioseq_set_Base::SetId (void) |
Assign a value to Id data member. More... | |
bool | CBioseq_set_Base::IsSetColl (void) const |
to identify a collection Check if a value has been assigned to Coll data member. More... | |
bool | CBioseq_set_Base::CanGetColl (void) const |
Check if it is safe to call GetColl method. More... | |
void | CBioseq_set_Base::ResetColl (void) |
Reset Coll data member. More... | |
const TColl & | CBioseq_set_Base::GetColl (void) const |
Get the Coll member data. More... | |
void | CBioseq_set_Base::SetColl (TColl &value) |
Assign a value to Coll data member. More... | |
TColl & | CBioseq_set_Base::SetColl (void) |
Assign a value to Coll data member. More... | |
bool | CBioseq_set_Base::IsSetLevel (void) const |
nesting level Check if a value has been assigned to Level data member. More... | |
bool | CBioseq_set_Base::CanGetLevel (void) const |
Check if it is safe to call GetLevel method. More... | |
void | CBioseq_set_Base::ResetLevel (void) |
Reset Level data member. More... | |
TLevel | CBioseq_set_Base::GetLevel (void) const |
Get the Level member data. More... | |
void | CBioseq_set_Base::SetLevel (TLevel value) |
Assign a value to Level data member. More... | |
TLevel & | CBioseq_set_Base::SetLevel (void) |
Assign a value to Level data member. More... | |
bool | CBioseq_set_Base::IsSetClass (void) const |
Check if a value has been assigned to Class data member. More... | |
bool | CBioseq_set_Base::CanGetClass (void) const |
Check if it is safe to call GetClass method. More... | |
void | CBioseq_set_Base::ResetClass (void) |
Reset Class data member. More... | |
void | CBioseq_set_Base::SetDefaultClass (void) |
Assign default value to Class data member. More... | |
TClass | CBioseq_set_Base::GetClass (void) const |
Get the Class member data. More... | |
void | CBioseq_set_Base::SetClass (TClass value) |
Assign a value to Class data member. More... | |
TClass & | CBioseq_set_Base::SetClass (void) |
Assign a value to Class data member. More... | |
bool | CBioseq_set_Base::IsSetRelease (void) const |
Check if a value has been assigned to Release data member. More... | |
bool | CBioseq_set_Base::CanGetRelease (void) const |
Check if it is safe to call GetRelease method. More... | |
void | CBioseq_set_Base::ResetRelease (void) |
Reset Release data member. More... | |
const TRelease & | CBioseq_set_Base::GetRelease (void) const |
Get the Release member data. More... | |
void | CBioseq_set_Base::SetRelease (const TRelease &value) |
Assign a value to Release data member. More... | |
void | CBioseq_set_Base::SetRelease (TRelease &&value) |
TRelease & | CBioseq_set_Base::SetRelease (void) |
Assign a value to Release data member. More... | |
bool | CBioseq_set_Base::IsSetDate (void) const |
Check if a value has been assigned to Date data member. More... | |
bool | CBioseq_set_Base::CanGetDate (void) const |
Check if it is safe to call GetDate method. More... | |
void | CBioseq_set_Base::ResetDate (void) |
Reset Date data member. More... | |
const TDate & | CBioseq_set_Base::GetDate (void) const |
Get the Date member data. More... | |
void | CBioseq_set_Base::SetDate (TDate &value) |
Assign a value to Date data member. More... | |
TDate & | CBioseq_set_Base::SetDate (void) |
Assign a value to Date data member. More... | |
bool | CBioseq_set_Base::IsSetDescr (void) const |
Check if a value has been assigned to Descr data member. More... | |
bool | CBioseq_set_Base::CanGetDescr (void) const |
Check if it is safe to call GetDescr method. More... | |
void | CBioseq_set_Base::ResetDescr (void) |
Reset Descr data member. More... | |
const TDescr & | CBioseq_set_Base::GetDescr (void) const |
Get the Descr member data. More... | |
void | CBioseq_set_Base::SetDescr (TDescr &value) |
Assign a value to Descr data member. More... | |
TDescr & | CBioseq_set_Base::SetDescr (void) |
Assign a value to Descr data member. More... | |
bool | CBioseq_set_Base::IsSetSeq_set (void) const |
Check if a value has been assigned to Seq_set data member. More... | |
bool | CBioseq_set_Base::CanGetSeq_set (void) const |
Check if it is safe to call GetSeq_set method. More... | |
void | CBioseq_set_Base::ResetSeq_set (void) |
Reset Seq_set data member. More... | |
const TSeq_set & | CBioseq_set_Base::GetSeq_set (void) const |
Get the Seq_set member data. More... | |
TSeq_set & | CBioseq_set_Base::SetSeq_set (void) |
Assign a value to Seq_set data member. More... | |
bool | CBioseq_set_Base::IsSetAnnot (void) const |
Check if a value has been assigned to Annot data member. More... | |
bool | CBioseq_set_Base::CanGetAnnot (void) const |
Check if it is safe to call GetAnnot method. More... | |
void | CBioseq_set_Base::ResetAnnot (void) |
Reset Annot data member. More... | |
const TAnnot & | CBioseq_set_Base::GetAnnot (void) const |
Get the Annot member data. More... | |
TAnnot & | CBioseq_set_Base::SetAnnot (void) |
Assign a value to Annot data member. More... | |
virtual void | CBioseq_set_Base::Reset (void) |
Reset the whole object. More... | |
CBioseq_set_Base::CBioseq_set_Base (const CBioseq_set_Base &) | |
CBioseq_set_Base & | CBioseq_set_Base::operator= (const CBioseq_set_Base &) |
CSeq_entry_Base::CSeq_entry_Base (void) | |
virtual | CSeq_entry_Base::~CSeq_entry_Base (void) |
CSeq_entry_Base::DECLARE_INTERNAL_TYPE_INFO () | |
virtual void | CSeq_entry_Base::Reset (void) |
Reset the whole object. More... | |
virtual void | CSeq_entry_Base::ResetSelection (void) |
Reset the selection (set it to e_not_set). More... | |
E_Choice | CSeq_entry_Base::Which (void) const |
Which variant is currently selected. More... | |
void | CSeq_entry_Base::CheckSelected (E_Choice index) const |
Verify selection, throw exception if it differs from the expected. More... | |
void | CSeq_entry_Base::ThrowInvalidSelection (E_Choice index) const |
Throw 'InvalidSelection' exception. More... | |
static string | CSeq_entry_Base::SelectionName (E_Choice index) |
Retrieve selection name (for diagnostic purposes). More... | |
void | CSeq_entry_Base::Select (E_Choice index, EResetVariant reset=eDoResetVariant) |
Select the requested variant if needed. More... | |
void | CSeq_entry_Base::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool) |
Select the requested variant if needed, allocating CObject variants from memory pool. More... | |
bool | CSeq_entry_Base::IsSeq (void) const |
Check if variant Seq is selected. More... | |
const TSeq & | CSeq_entry_Base::GetSeq (void) const |
Get the variant data. More... | |
TSeq & | CSeq_entry_Base::SetSeq (void) |
Select the variant. More... | |
void | CSeq_entry_Base::SetSeq (TSeq &value) |
Select the variant and set its data. More... | |
bool | CSeq_entry_Base::IsSet (void) const |
Check if variant Set is selected. More... | |
const TSet & | CSeq_entry_Base::GetSet (void) const |
Get the variant data. More... | |
TSet & | CSeq_entry_Base::SetSet (void) |
Select the variant. More... | |
void | CSeq_entry_Base::SetSet (TSet &value) |
Select the variant and set its data. More... | |
CSeq_entry_Base::CSeq_entry_Base (const CSeq_entry_Base &) | |
CSeq_entry_Base & | CSeq_entry_Base::operator= (const CSeq_entry_Base &) |
void | CSeq_entry_Base::DoSelect (E_Choice index, CObjectMemoryPool *pool=0) |
Variables | |
Uint4 | CBioseq_set_Base::m_set_State [1] |
CRef< TId > | CBioseq_set_Base::m_Id |
CRef< TColl > | CBioseq_set_Base::m_Coll |
int | CBioseq_set_Base::m_Level |
EClass | CBioseq_set_Base::m_Class |
string | CBioseq_set_Base::m_Release |
CRef< TDate > | CBioseq_set_Base::m_Date |
CRef< TDescr > | CBioseq_set_Base::m_Descr |
list< CRef< CSeq_entry > > | CBioseq_set_Base::m_Seq_set |
list< CRef< CSeq_annot > > | CBioseq_set_Base::m_Annot |
E_Choice | CSeq_entry_Base::m_choice |
static const char *const | CSeq_entry_Base::sm_SelectionNames [] |
NCBI_NS_NCBI::CSerialObject * | CSeq_entry_Base::m_object |
typedef list< CRef< CSeq_annot > > CBioseq_set_Base::TAnnot |
Definition at line 137 of file Bioseq_set_.hpp.
typedef EClass CBioseq_set_Base::TClass |
Definition at line 132 of file Bioseq_set_.hpp.
typedef CDbtag CBioseq_set_Base::TColl |
Definition at line 130 of file Bioseq_set_.hpp.
typedef CDate CBioseq_set_Base::TDate |
Definition at line 134 of file Bioseq_set_.hpp.
typedef CSeq_descr CBioseq_set_Base::TDescr |
Definition at line 135 of file Bioseq_set_.hpp.
typedef CObject_id CBioseq_set_Base::TId |
Definition at line 129 of file Bioseq_set_.hpp.
typedef int CBioseq_set_Base::TLevel |
Definition at line 131 of file Bioseq_set_.hpp.
Definition at line 152 of file Bioseq_set_.hpp.
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Definition at line 87 of file Bioseq_set_.hpp.
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Definition at line 75 of file Seq_entry_.hpp.
typedef string CBioseq_set_Base::TRelease |
Definition at line 133 of file Bioseq_set_.hpp.
typedef CBioseq CSeq_entry_Base::TSeq |
Definition at line 145 of file Seq_entry_.hpp.
typedef list< CRef< CSeq_entry > > CBioseq_set_Base::TSeq_set |
Definition at line 136 of file Bioseq_set_.hpp.
typedef CBioseq_set CSeq_entry_Base::TSet |
Definition at line 146 of file Seq_entry_.hpp.
Choice variants.
Enumerator | |
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e_not_set | No variant selected. |
e_Seq | |
e_Set |
Definition at line 87 of file Seq_entry_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Set+1 |
Definition at line 93 of file Seq_entry_.hpp.
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Enumerator | |
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e__allMandatory | |
e_id | |
e_coll | |
e_level | |
e_class | |
e_release | |
e_date | |
e_descr | |
e_seq_set | |
e_annot |
Definition at line 140 of file Bioseq_set_.hpp.
Definition at line 97 of file Bioseq_set_.hpp.
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Check if it is safe to call GetAnnot method.
Definition at line 775 of file Bioseq_set_.hpp.
Referenced by CAttachedHandles::Attach(), and ReplaceWellknownSeqs().
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Check if it is safe to call GetClass method.
Definition at line 611 of file Bioseq_set_.hpp.
Referenced by CWithdrawSequences::GetNames(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::TakeFromSet(), and CTopLevelSeqEntryContext::x_InitSeqs().
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Check if it is safe to call GetColl method.
Definition at line 543 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetColl().
Referenced by CBioseq_set_Base::GetColl().
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Check if it is safe to call GetDate method.
Definition at line 708 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetDate().
Referenced by CBioseq_set_Base::GetDate().
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Check if it is safe to call GetDescr method.
Definition at line 729 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetDescr().
Referenced by CDiscrepancyContext::AutofixBioseq_set(), CBioseq_set_Base::GetDescr(), and CDiscrepancyContext::PopulateSeqSet().
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Check if it is safe to call GetId method.
Definition at line 522 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetId().
Referenced by CBioseq_set_Base::GetId().
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Check if it is safe to call GetLevel method.
Definition at line 564 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetLevel().
Referenced by CBioseq_set_Base::GetLevel().
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Check if it is safe to call GetRelease method.
Definition at line 661 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetRelease().
Referenced by CBioseq_set_Base::GetRelease().
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Check if it is safe to call GetSeq_set method.
Definition at line 750 of file Bioseq_set_.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), FlattenBioseqSet(), get_parent_seqset(), CDiscrepancyContext::ParseObject(), CWithdrawSequences::PopulateSet(), CReorderSequencesDlg::PopulateSet(), CSegregateSetsBase::PopulateSet(), ReplaceWellknownSeqs(), CSegregateSetsBase::TakeFromSet(), CFlatGatherer::x_GatherCDSReferences(), CRemoteBlast::x_InitQueries(), and CExportStrategy::x_Process_Query().
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END_CLASS_INFO CBioseq_set_Base::CBioseq_set_Base | ( | void | ) |
Definition at line 206 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_set_State.
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 234 of file Seq_entry_.hpp.
References CSeq_entry_Base::m_choice, and CSeq_entry_Base::ThrowInvalidSelection().
Referenced by CSeq_entry_Base::GetSeq(), and CSeq_entry_Base::GetSet().
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END_CHOICE_INFO CSeq_entry_Base::CSeq_entry_Base | ( | void | ) |
Definition at line 160 of file Seq_entry_.cpp.
CBioseq_set_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_entry_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
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Definition at line 71 of file Seq_entry_.cpp.
References CObject::AddReference(), CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CSeq_entry_Base::m_choice, and CSeq_entry_Base::m_object.
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Access to EClass's attributes (values, names) as defined in spec.
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Get the Annot member data.
Definition at line 781 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Annot.
Referenced by AddFeat(), CDiscrepancyContext::AutofixBioseq_set(), CheckFeatSeqLoc(), CBlobSplitterImpl::CopySkeleton(), CDiscrepancyContext::PopulateSeqSet(), CBioseq_set_Info::sx_ShallowCopy(), CValidError_bioseqset::ValidateBioseqSet(), CNewCleanup_imp::x_CollapseSet(), CSeqMasterIndex::x_InitSeqs(), and CNewCleanup_imp::x_RemoveEmptyFeatureTables().
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Get the Class member data.
Definition at line 630 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Class.
Referenced by CTbl2AsnApp::AddAnnots(), AddChromosomeNoLocation(), AddSeqdescToSeqEntryRecursively(), AddTitle(), CSourceModParser::ApplyAllMods(), CTable2AsnContext::ApplyComments(), CTable2AsnContext::ApplyCreateUpdateDates(), seqsubmit_split::CSeqEntryHelper::BuildObject(), CConvertSetTypeDlg::ChangeNotify(), CValidError_bioseqset::CheckForInconsistentBiomols(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CFeatureTableReader::ConvertNucSetToSet(), CBlobSplitterImpl::CopySkeleton(), sequpd::FixCollidingIDs_Bioseq(), CFlatFileGenerator::Generate(), CEditObjectSet::GetEditCommand(), CBioseq_set::GetGenomicFromGenProdSet(), CBioseq_setHandler::GetLabel(), CBioseq_set::GetLabel(), CBioseq_set::GetMasterFromSegSet(), CWithdrawSequences::GetNames(), CBioseq_set::GetNucFromNucProtSet(), CGuiObjectInfoBioseq_set::GetSubtype(), CDeflineProcess::IndexedProcess(), CValidError_imp::IsHugeSet(), MoveAnnotToTop(), MoveBiomolToTop(), CSegregateSetsBase::MoveDescrToEntries(), CBioseq_set::NeedsDocsumTitle(), seqsubmit_split::NeedToProcess(), CConvertSetTypeDlg::OnTreebookSelChanged(), CDiscrepancyContext::ParseObject(), CReorderSequencesDlg::ReadBioseq(), CRemoveSet::remove_sets_from_set(), CRemoveSet::RemoveOneSet(), RevComp(), s_CountTopSetSiblings(), s_GetBioseq_setContent(), s_GetBioseq_setType(), s_GetGenProdContent(), s_GetIdLabel(), s_GetNucProtContent(), s_GetSegsetContent(), s_GetSeqFromSet(), s_HasUnprocessedCdregions(), s_IsValidNPSubset(), s_SetDBLinkDesc(), sApplyDescriptors(), CNewCleanup_imp::SeqsetBC(), CValidError_bioseqset::SetShouldNotHaveMolInfo(), CBioseq_set_Info::sx_ShallowCopy(), CSegregateSetsBase::TakeFromSet(), TrimEntry(), CDeflineProcess::UnindexedProcess(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqParts(), CValidError_bioseqset::ValidateSetElements(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CNewCleanup_imp::x_ChangePopToPhy(), CTopLevelSeqEntryContext::x_InitSeqs(), CNewCleanup_imp::x_MovePopPhyMutPub(), CCleanupApp::x_ProcessHugeFileBlob(), CNewCleanup_imp::x_RemoveNestedNucProtSet(), CValidError_bioseqset::x_ValidateSetDescriptors(), CFeatureTableReader::xCheckIfNeedConversion(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), and CFeatureTableReader::xParseCdregions().
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Get the Coll member data.
Definition at line 549 of file Bioseq_set_.hpp.
References CBioseq_set_Base::CanGetColl(), CBioseq_set_Base::m_Coll, and CSerialObject::ThrowUnassigned().
Referenced by CBlobSplitterImpl::CopySkeleton(), and CBioseq_set_Info::sx_ShallowCopy().
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Get the Date member data.
Definition at line 714 of file Bioseq_set_.hpp.
References CBioseq_set_Base::CanGetDate(), CBioseq_set_Base::m_Date, and CSerialObject::ThrowUnassigned().
Referenced by CBlobSplitterImpl::CopySkeleton(), and CBioseq_set_Info::sx_ShallowCopy().
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Get the Descr member data.
Definition at line 735 of file Bioseq_set_.hpp.
References CBioseq_set_Base::CanGetDescr(), CBioseq_set_Base::m_Descr, and CSerialObject::ThrowUnassigned().
Referenced by CDiscrepancyContext::AutofixBioseq_set(), BOOST_AUTO_TEST_CASE(), BuildProtBioseqSet(), CollectDescriptors(), CBlobSplitterImpl::CopySkeleton(), FixDupDates(), FixEmblUpdateDates(), GetDescrPointer(), CEditObjectSet::GetEditCommand(), CTable2AsnContext::GetOrgName(), GetPDBBlockFromSeqEntry(), CRemoveSet::MoveDescrToEntries(), CSegregateSetsBase::MoveDescrToEntries(), MoveSourceDescrToTop(), CDiscrepancyContext::PopulateSeqSet(), CDUpdater::reformatBioseq(), CSequenceEditingEventHandler::SaveDescriptors(), CValidError_bioseqset::SetShouldNotHaveMolInfo(), CValidError_bioseqset::ShouldHaveNoDblink(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidateSetTitle(), CNewCleanup_imp::x_ClearEmptyDescr(), CNewCleanup_imp::x_CollapseSet(), CSeqMasterIndex::x_InitSeqs(), CAgpconvertApplication::x_LoadTemplate(), CNewCleanup_imp::x_MoveNpDBlinks(), CNewCleanup_imp::x_MoveNpPub(), CNewCleanup_imp::x_MovePopPhyMutPub(), CNewCleanup_imp::x_RemoveDupBioSource(), CValidError_bioseqset::x_ValidateSetDescriptors(), and seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry().
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Get the Id member data.
Definition at line 528 of file Bioseq_set_.hpp.
References CBioseq_set_Base::CanGetId(), CBioseq_set_Base::m_Id, and CSerialObject::ThrowUnassigned().
Referenced by CBlobSplitterImpl::CopySkeleton(), CBioseq_set_Info::sx_ShallowCopy(), and CSplitDataLoader::x_SplitSet().
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Get the Level member data.
Definition at line 577 of file Bioseq_set_.hpp.
References CBioseq_set_Base::CanGetLevel(), CBioseq_set_Base::m_Level, and CSerialObject::ThrowUnassigned().
Referenced by CBlobSplitterImpl::CopySkeleton(), CBioseq_set_Info::sx_ShallowCopy(), TrimEntry(), and CGC_Assembly_Parser::x_InitSeq_entry().
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Get the Release member data.
Definition at line 667 of file Bioseq_set_.hpp.
References CBioseq_set_Base::CanGetRelease(), CBioseq_set_Base::m_Release, and CSerialObject::ThrowUnassigned().
Referenced by CBlobSplitterImpl::CopySkeleton(), CBioseq_set_Info::sx_ShallowCopy(), and TrimEntry().
const CSeq_entry_Base::TSeq & CSeq_entry_Base::GetSeq | ( | void | ) | const |
Get the variant data.
Definition at line 102 of file Seq_entry_.cpp.
References CSeq_entry_Base::CheckSelected(), CSeq_entry_Base::e_Seq, and CSeq_entry_Base::m_object.
Referenced by AddChromosomeNoLocation(), AddFeat(), AddLocalIdUserObjects(), CGBProjectHelper::AddProjectItemsFromRID(), CFeatureTableReader::AddProteins(), AddProtFeat(), AddToDeltaSeq(), CAlignmentAssistant::AdjustBioseq(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CClearKeywords::ApplyToCSeq_entry(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), BOOST_AUTO_TEST_CASE(), BuildGoodByteGraph(), CheckAdjustStart(), CheckAdjustStop(), CheckMiscPartialErrors(), CheckOneSpecificHost(), CollectDescriptors(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CopyBioseqWithType(), CopySeqIdsOfType(), CBlobSplitterImpl::CopySkeleton(), CPsiBl2SeqTestFixture::CPsiBl2SeqTestFixture(), CMolInfoEditDlg::CreateNewMolInfo(), CGuiObjectInfoSeq_entry::CreateObject(), CCmdAddSeqEntry::Execute(), ExtractBioseq(), FindNucInSeqEntry(), FlattenBioseqSet(), fta_remove_cleanup_user_object(), CDiscrepancyPanel::GetAccessionForObject(), GetAccessionFromObjects(), CDUpdater::GetAllIdsFromSeqEntry(), CSeq_entry::GetAnnot(), GetBioseq(), GetBioseqWithType(), CEditSequenceEnds::GetCommand(), CEditSeqEndsWithAlign::GetCommand(), AlignmentCollection::GetDefline(), CSeq_entry::GetDescr(), GetDescrPointer(), GetGoodSeqEntryWithFeatureIds(), CSeq_entryHandler::GetLabel(), CSeq_entry::GetLabel(), CWGSDb_Impl::GetMasterDescrEntry(), CWGSDb_Impl::GetMasterGi(), CWithdrawSequences::GetNames(), GetNcbieaaString(), CFastaBioseqSource::GetNext(), CMaskFastaReader::GetNextSequence(), CBioseq_set::GetNucFromNucProtSet(), CDUpdater::GetOneBioseqFromSeqEntry(), GetPDBBlockFromSeqEntry(), CPssm::GetQueryLength(), CPssm::GetQuerySequenceData(), GetResidueAtPosition(), GetSeqLength(), GetSeqsStatus(), TaxTreeData::GetTaxIDForSequence(), HasRepairedIDs(), HasSeqIdOfType(), CViewGraphic::InitView(), CVcfTableView::InitView(), CDiscrepancyPanel::InvalidObject(), CSeq_entry::IsSetAnnot(), CSeq_entry::IsSetDescr(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CReadBlastApp::less_seq(), CFastaObjectLoader::LoadFromStream(), CTblastnNode::Main(), MakeEntryForDeltaConversion(), CSequesterSets::OnAccept(), CEditSequence::OnAccept(), CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked(), seqsubmit_split::SCompare< SLongestFirstCompare >::operator()(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), CTbl2AsnApp::ProcessHugeFile(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), CFastaReaderEx::ReadDeltaFasta(), ReplaceWellknownSeqs(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CLocalFinderApp::Run(), CWinMaskDemoApplication::Run(), CAgpconvertApplication::Run(), CVDBTblastnApp::Run(), s_AddCDS(), s_AddSeqDataToPssm(), s_CollectCollidingIDs_Entry(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CreateQueryMap(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_ReadAndTestQueryFromString_CFastaReader(), s_RemoveAnnotsFromEntry(), PssmScorer::score(), SetCompleteness(), CNewCleanup_imp::SetGlobalFlags(), CValidErrorSuppress::SetSuppressedCodes(), ShowOrgRef(), CSegregateSetsBase::TakeFromSet(), TestCds(), TestCdsFromLastBioseq(), TestCdsFromLastBioseqOutsideAlign(), TestCdsFromLastBioseqWithCodeBreak(), TestCdsWithCodeBreak(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFuseAbuttingIntervals(), TestOneGapSeq(), TestOrderedLoc(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), TestPartialWhenCutStopDoNotExtend(), TestPointLocInside(), TestPointLocOutside(), TestTrnaAnticodon(), TestTrnaAnticodonFromLastBioseq(), TestTwoIntCdsFromLastBioseqOutsideAlign(), TestTwoIntCdsOnMinusStrand(), TestUTRPair(), TrimEntry(), SequenceSet::UnpackSeqEntry(), CValidError_imp::Validate(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_imp::ValidateBioSource(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CConversionApp::Write(), CFastaOstream::Write(), CSequenceUpdater::x_AdjustProteinFeature(), CCountryFixup::x_ApplyToDescriptors(), CBlastFormatterApp::x_BuildQueryFromPssm(), CBlastFormatterVdbApp::x_BuildQueryFromPssm(), CDesktopDataBuilder::x_CreateSet(), CPrimeCacheApplication::x_ExtractAndIndex(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CRemoteBlast::x_ExtractQueryIds(), CBlastFastaInputSource::x_FastaToSeqLoc(), CAsnCacheTestApplication::x_FindAnnotated(), CSraInputSource::x_GetNextSeq_loc(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), CBamRefSeqInfo::x_LoadRangesCov(), CMakeProfileDBApp::x_MakeVol(), CBioseq_Info::x_ParentAttach(), CLDS2_Manager::x_ParseFile(), CPrimeCacheApplication::x_Process_Fasta(), CCleanupApp::x_ProcessTraditionally(), CSplignApp::x_ReadFastaSetId(), CASN1InputSourceOMF::x_ReadOneSeq(), CMacroFunction_UpdateProteinSeqs::x_ReadUpdateSeqs(), CNgAlignApp::x_RecurseSeqEntry(), CTblastnApp::x_RunMTBySplitDB(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), CCDSTranslationPanel::x_SetProtein(), CPrimeCacheApplication::x_StripSeqEntry(), CMakeProfileDBApp::x_UpdateCobalt(), CSequenceUpdater::x_UpdateProteinID(), CAgpConverter::x_VerifyComponents(), CFeatureTableReader::xAddProteinToSeqEntry(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xMergeCDSFeatures_impl().
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Get the Seq_set member data.
Definition at line 756 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Seq_set.
Referenced by CFeatureTableReader::AddProteins(), CDiscrepancyContext::AutofixBioseq_set(), BioseqSetDescriptorPropagateUp(), CSequesterSets::BioseqSetDescriptorPropagateUp(), BOOST_AUTO_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildGoodEcoSetWithAlign(), CConvertSetTypeDlg::ChangeNotify(), Check3Extend(), Check5Extend(), CValidError_bioseqset::CheckForImproperlyNestedSets(), CollectDescriptors(), CCdCore::CopyBioseqForSeqId(), CopyBioseqWithType(), CopySeqIdsOfType(), CBlobSplitterImpl::CopySkeleton(), DeleteProteinAndRenormalizeNucProtSet(), CCdCore::EraseSequences(), CCmdInsertBioseqSet::Execute(), ExtractBioseq(), FetchSequenceViaHTTP(), FindNucInSeqEntry(), FlattenBioseqSet(), CScore_CdsInternalStops::Get(), CDUpdater::GetAllIdsFromSeqEntry(), CCdCore::GetBioseqWithSeqId(), CCdCore::GetDefline(), CBioseq_set::GetGenomicFromGenProdSet(), CCdCore::GetGIFromSequenceList(), CBioseq_set::GetLabel(), CBioseq_set::GetMasterFromSegSet(), CCdCore::GetMmdbId(), CBlastInputOMF::GetNextSeqBatch(), CBioseq_set::GetNucFromNucProtSet(), CBlast4_queries::GetNumQueries(), CFastaIOWrapper::GetNumRead(), CDUpdater::GetOneBioseqFromSeqEntry(), GetPDBBlockFromSeqEntry(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), CCdCore::GetSeqEntryForIndex(), CCdCore::GetSeqEntryForRow(), CCdCore::GetSeqIDForIndex(), CCdCore::GetSeqIDs(), CCdCore::GetSeqIndex(), GetSourceDescriptors(), CSraRun::GetSpotEntry(), HasRepairedIDs(), HasSeqIdOfType(), CValidError_bioseqset::IsCDSProductInGPS(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CMagicBlastThread::Main(), MoveBiomolToTop(), SBlobInserter::operator()(), CDiscrepancyContext::ParseObject(), CReorderSequencesDlg::PopulateSet(), CTabularFormatter_StopCodonChanges::Print(), CBiosampleChkApp::ProcessSet(), CTLSHandler::ProcessSet(), PropagateDescriptor(), CConversionApp::Read(), CFastaReader::ReadAlignedSet(), UpdateViewer::ReadSequencesFromFile(), CFastaReader::ReadSet(), CCleanup::RenormalizeNucProtSets(), RevComp(), s_BuildBadEcNumberEntry(), s_CollectSeqIds(), s_CountTopSetSiblings(), s_CreateQueryMap(), s_DescriptorPropagateDown(), s_GetBioseq_setContent(), s_GetIdLabel(), s_GetJustNucSeqEntry(), s_GetSeqFromSet(), s_GetSourceDescriptors(), s_HasTopSetSiblings(), s_ImportQueries(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), s_ScanWhilePossibleNPSet(), CAgpConverter::SetComponentsBioseqSet(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), TestCollidingAccessionFixes(), TestFeatInsideGap(), CSplitCacheApp::TestSplitBioseq(), TrimEntry(), CCmdAddCDS::Unexecute(), CCmdCreateCDS::Unexecute(), CCmdInsertBioseqSet::Unexecute(), SequenceSet::UnpackSeqSet(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CValidError_bioseqset::ValidateSetElements(), CFastaOstream::Write(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CDescPlacementPanel::x_AddToStrings(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_CollapseSet(), CPrimeCacheApplication::x_ExtractAndIndex(), CFlatGatherer::x_GatherCDSReferences(), CRemoteBlast::x_InitQueries(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), x_IsEmptyCDD(), CAgpconvertApplication::x_LoadTemplate(), CNewCleanup_imp::x_MovePopPhyMutPub(), CExportStrategy::x_Process_Query(), CNgAlignApp::x_RecurseSeqEntry(), CNewCleanup_imp::x_RemoveNestedGenBankSet(), CNewCleanup_imp::x_RemoveNestedNucProtSet(), CPrimeCacheApplication::x_StripSeqEntry(), CCmdInsertBioseqSet::x_TransferSeqSet(), CFormatGuessEx::x_TryFasta(), and CMultiReader::xApplyTemplate().
const CSeq_entry_Base::TSet & CSeq_entry_Base::GetSet | ( | void | ) | const |
Get the variant data.
Definition at line 124 of file Seq_entry_.cpp.
References CSeq_entry_Base::CheckSelected(), CSeq_entry_Base::e_Set, and CSeq_entry_Base::m_object.
Referenced by CAddStructuredCommentKeyword::add_to_existing_genbank(), CTbl2AsnApp::AddAnnots(), AddChromosomeNoLocation(), AddFeat(), AddFeatAnnotToSeqEntry(), AddLocalIdUserObjects(), CFeatureTableReader::AddProteins(), AddSeqdescToSeqEntryRecursively(), AddTitle(), CTable2AsnContext::ApplyCreateUpdateDates(), CSetGlobalRefGeneStatus::ApplyToCSeq_entry(), CClearKeywords::ApplyToCSeq_entry(), CRemoveBankitComment::ApplyToCSeq_entry(), CRemoveGenomeProjectsDB::ApplyToCSeq_entry(), CRemoveStructuredComment::ApplyToCSeq_entry(), CRemoveSeqAnnot::ApplyToCSeq_entry(), CConvertComment::ApplyToCSeq_entry(), CModifyStructuredComment::ApplyToCSeq_entry(), CRemoveUnverified::ApplyToCSeq_entry(), CRemoveStructuredCommentKeyword::ApplyToCSeq_entry_genbank(), CChangeStructuredCommentKeyword::ApplyToCSeq_entry_user(), CReorderStructuredComment::ApplyToCSeq_entry_user(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), CAttachedHandles::Attach(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), CMacroBioData_SeqSetIter::BuildEditedObject(), BuildGoodEcoSetWithAlign(), seqsubmit_split::CSeqEntryHelper::BuildObject(), BuildSetAlign(), BuildSetDendiagAlign(), Check3Extend(), Check5Extend(), CollectDescriptors(), Convert_Seq_entry_Bioseq_set(), Convert_Seq_id_Bioseq_set(), CFeatureTableReader::ConvertNucSetToSet(), CSequenceEditingEventHandler::ConvertSetType(), CCdCore::CopyBioseqForSeqId(), CopyBioseqWithType(), CopySeqIdsOfType(), CBlobSplitterImpl::CopySkeleton(), CreateEditorForObject(), CGuiObjectInfoSeq_entry::CreateObject(), CCdCore::EraseSequences(), CStrainRequest::ExploreStrainsByTaxname(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), ExtractBioseq(), FetchSequenceViaHTTP(), FindNucInSeqEntry(), sequpd::FixCollidingIDs_Bioseq(), FlattenBioseqSet(), fta_remove_cleanup_user_object(), CValidError_imp::GatherTentativeName(), get_parent_seqset(), GetAccessionFromObjects(), CDUpdater::GetAllIdsFromSeqEntry(), CValidError_imp::GetAncestor(), CSeq_entry::GetAnnot(), CCdCore::GetBioseqWithSeqId(), CCdCore::GetDefline(), CExportTableDlg::GetDesc(), CUnculTaxTool::GetDesc(), CAddFluComments::GetDesc(), CSeq_entry::GetDescr(), GetDescrPointer(), CCdCore::GetGIFromSequenceList(), CSeq_entryHandler::GetLabel(), CSeq_entry::GetLabel(), CCdCore::GetMmdbId(), CWithdrawSequences::GetNames(), CBioseq_set::GetNucFromNucProtSet(), CFastaIOWrapper::GetNumRead(), CDUpdater::GetOneBioseqFromSeqEntry(), CTable2AsnContext::GetOrgName(), CBioseq::GetParentSet(), CBioseq_set::GetParentSet(), GetPDBBlockFromSeqEntry(), CMacroBioData_SeqSetIter::GetScopedObject(), CCdCore::GetSeqEntryForIndex(), CCdCore::GetSeqEntryForRow(), CCdCore::GetSeqIDForIndex(), CCdCore::GetSeqIDs(), CCdCore::GetSeqIndex(), GetSourceDescriptors(), HasRepairedIDs(), HasSeqIdOfType(), CBioseqEditor::IsEditable(), CSeq_entry::IsSetAnnot(), CSeq_entry::IsSetDescr(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), MoveAnnotToTop(), MoveBiomolToTop(), seqsubmit_split::NeedToProcess(), CSequesterSets::OnAccept(), SBlobInserter::operator()(), seqsubmit_split::SCompare< SLongestFirstCompare >::operator()(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), CTbl2AsnApp::ProcessAlignmentFile(), CTbl2AsnApp::ProcessHugeFile(), CFastaReader::ReadAlignedSet(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), UpdateViewer::ReadSequencesFromFile(), CFastaReader::ReadSet(), CDUpdater::reformatBioseq(), CCleanup::RemoveNcbiCleanupObject(), RemoveTitlesSeqEntry(), RemoveUserObjectType(), CCleanup::RenormalizeNucProtSets(), RevComp(), CMacroBioData_SeqSetIter::RunDeleteCommand(), CMacroBioData_SeqSetIter::RunEditCommand(), s_BuildBadEcNumberEntry(), s_CollectCollidingIDs_Entry(), s_CollectPubDescriptorLabels(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CountTopSetSiblings(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetJustNucSeqEntry(), s_GetSourceDescriptors(), s_HasUnprocessedCdregions(), s_IsHtgInSep(), s_RemoveAnnotsFromEntry(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), CRemoveSeqFromAlignDlg::SearchSeq_entry(), CNewCleanup_imp::SetGlobalFlags(), CValidErrorSuppress::SetSuppressedCodes(), ShowOrgRef(), sx_ComesBefore(), CSegregateSetsBase::TakeFromSet(), TestCollidingAccessionFixes(), TestFeatInsideGap(), CSplitCacheApp::TestSplitBioseq(), TrimEntry(), CCmdAddSeqEntry::Unexecute(), CCmdInsertBioseqSet::Unexecute(), CDeflineProcess::UnindexedProcess(), SequenceSet::UnpackSeqEntry(), CValidError_imp::Validate(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqParts(), CConversionApp::Write(), CFastaOstream::Write(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CDescPlacementPanel::x_AddToStrings(), CAppendModToOrg::x_ApplyToDescriptors(), CApplyGCode::x_ApplyToDescriptors(), CCountryConflict::x_ApplyToDescriptors(), CCountryFixup::x_ApplyToDescriptors(), CLatLonTool::x_ApplyToDescriptors(), IModifyBiosourceQuals::x_ApplyToDescriptors(), IPubDescEditor::x_ApplyToDescriptors(), IRemovePubs::x_ApplyToDescriptors(), CRemoveUnreviewed::x_ApplyToSeq_entry(), CRemoveDescDlg::x_ApplyToSeq_entry(), CStrainRequest::x_CollectStrainsForRecord(), CDesktopDataBuilder::x_CreateSet(), CPrimeCacheApplication::x_ExtractAndIndex(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CRemoteBlast::x_ExtractQueryIds(), CAsnCacheTestApplication::x_FindAnnotated(), CTaxValidationAndCleanup::x_GatherSources(), CGC_Assembly_Parser::x_InitSeq_entry(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), x_IsEmptyCDD(), CAgpconvertApplication::x_LoadTemplate(), CBioseq_set_Info::x_ParentAttach(), CStrainSerotypeInfluenza::x_ParseDescriptors(), CCleanupApp::x_ProcessHugeFileBlob(), CCleanupApp::x_ProcessTraditionally(), CNgAlignApp::x_RecurseSeqEntry(), CNewCleanup_imp::x_RemoveDupBioSource(), CMacroBioData_SeqSetIter::x_SetDefaultObjectInfo(), CStrainSerotypeInfluenza::x_TestEntryForParsing(), CFormatGuessEx::x_TryFasta(), CMultiReader::xApplyTemplate(), CFeatureTableReader::xCheckIfNeedConversion(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), CFeatureTableReader::xParseCdregions(), and CTbl2AsnApp::xProcessOneFile().
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Check if variant Seq is selected.
Seq type is defined as 'typedef CBioseq TSeq'.
Definition at line 257 of file Seq_entry_.hpp.
References CSeq_entry_Base::e_Seq, and CSeq_entry_Base::m_choice.
Referenced by CTbl2AsnApp::AddAnnots(), AddChromosomeNoLocation(), AddFeat(), AddFeatAnnotToSeqEntry(), AddGoodPub(), AddGoodSource(), AddLocalIdUserObjects(), CGBProjectHelper::AddProjectItemsFromRID(), CFeatureTableReader::AddProteins(), AddRefGeneTrackingUserObject(), AddSeqdescToSeqEntryRecursively(), AddSource(), AddTitle(), AdjustProtFeatForNucProtSet(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CClearKeywords::ApplyToCSeq_entry(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), BOOST_AUTO_TEST_CASE(), ChangeId(), ClearFocus(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CopyBioseqWithType(), CopySeqIdsOfType(), CBlobSplitterImpl::CopySkeleton(), CMolInfoEditDlg::CreateNewMolInfo(), CGuiObjectInfoSeq_entry::CreateObject(), CCmdAddSeqEntry::Execute(), FetchSequenceViaHTTP(), FindNucInSeqEntry(), FlattenBioseqSet(), fta_get_user_object(), fta_remove_cleanup_user_object(), g_ApplyDescriptors(), get_parent_seqset(), CDiscrepancyPanel::GetAccessionForObject(), GetAccessionFromObjects(), CDUpdater::GetAllIdsFromSeqEntry(), GetBioseqWithType(), AlignmentCollection::GetDefline(), GetDescrPointer(), CWGSDb_Impl::GetMasterDescrEntry(), CWithdrawSequences::GetNames(), GetNcbieaaString(), CFastaBioseqSource::GetNext(), CMaskFastaReader::GetNextSequence(), CBioseq_set::GetNucFromNucProtSet(), CDUpdater::GetOneBioseqFromSeqEntry(), CTable2AsnContext::GetOrgName(), GetPDBBlockFromSeqEntry(), GetResidueAtPosition(), GetSeqsStatus(), TaxTreeData::GetTaxIDForSequence(), HasRepairedIDs(), HasSeqIdOfType(), IdFromEntry(), CViewGraphic::InitView(), CVcfTableView::InitView(), CDiscrepancyPanel::InvalidObject(), CViewGraphicFactory::IsCompatibleWith(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CwxDemoAlignTableFrame::LoadFile(), CwxDemoFeatureTableFrame::LoadFile(), CFastaObjectLoader::LoadFromStream(), CTblastnNode::Main(), CTable2AsnContext::MergeSeqDescr(), CTable2AsnContext::MergeWithTemplate(), MoveSourceDescrToTop(), seqsubmit_split::NeedToProcess(), CSequesterSets::OnAccept(), CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked(), SBlobInserter::operator()(), seqsubmit_split::SCompare< SLongestFirstCompare >::operator()(), CWinMaskUtil::CInputBioseq_CI::operator++(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), CRemoteUpdater::PostProcessPubs(), CTbl2AsnApp::ProcessHugeFile(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), CFastaReaderEx::ReadDeltaFasta(), CBasicFastaWrapper::ReadFile(), UpdateViewer::ReadSequencesFromFile(), CFeature_table_reader::ReadSequinFeatureTables(), CCachedSequence::RegisterIds(), RemoveDbxref(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RemoveNcbiCleanupObject(), CReadBlastApp::RemoveProblems(), RemoveUserObjectType(), ReplaceWellknownSeqs(), ResetOrgname(), RevComp(), CPsiBlastApp::Run(), CVDBTblastnApp::Run(), s_CollectCollidingIDs_Entry(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CountTopSetSiblings(), s_FastaStringToBioseq(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetJustNucSeqEntry(), s_MoveProteinSpecificFeats(), s_RemoveAnnotsFromEntry(), s_UpdateFeatureIds(), ScanFastaFile(), SeqEntryFromSeqSubmit(), SetChromosome(), SetCommon(), SetCompleteness(), SetDbxref(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), CNewCleanup_imp::SetGlobalFlags(), SetLineage(), SetMGcode(), SetNucProtSetProductName(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), CTable2AsnContext::SetSeqId(), SetSubSource(), CValidErrorSuppress::SetSuppressedCodes(), SetTaxname(), SetTaxon(), SetTransgenic(), ShowOrgRef(), SimplifySeqEntryForCD(), CSegregateSetsBase::TakeFromSet(), SequenceSet::UnpackSeqEntry(), UnpackSeqEntry(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_imp::ValidateBioSource(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CDescPlacementPanel::x_AddToStrings(), CCountryFixup::x_ApplyToDescriptors(), CBlastFormatterApp::x_BuildQueryFromPssm(), CBlastFormatterVdbApp::x_BuildQueryFromPssm(), CPrimeCacheApplication::x_ExtractAndIndex(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CRemoteBlast::x_ExtractQueryIds(), CAsnCacheTestApplication::x_FindAnnotated(), CSequenceUpdater::x_FixIDInNewEntry(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), CSplitDataLoader::x_LoadData(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CAgpconvertApplication::x_LoadTemplate(), CNewCleanup_imp::x_MoveNpDBlinks(), CLDS2_Manager::x_ParseFile(), CSequenceUpdater::x_PrepareNewEntry(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CMacroFunction_UpdateProteinSeqs::x_ReadUpdateSeqs(), CNgAlignApp::x_RecurseSeqEntry(), CNewCleanup_imp::x_RemovePub(), CTblastnApp::x_RunMTBySplitDB(), CHugeFileDemoApp::x_ShowSeqSizes(), CPrimeCacheApplication::x_StripSeqEntry(), CMakeProfileDBApp::x_UpdateCobalt(), CCdregionValidator::x_ValidateTrans(), CFeatureTableReader::xConvertSeqIntoSeqSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), and CFeatureTableReader::xMergeCDSFeatures_impl().
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Check if variant Set is selected.
Set type is defined as 'typedef CBioseq_set TSet'.
Definition at line 263 of file Seq_entry_.hpp.
References CSeq_entry_Base::e_Set, and CSeq_entry_Base::m_choice.
Referenced by CAddStructuredCommentKeyword::add_to_existing_genbank(), AddChromosomeNoLocation(), AddFeat(), AddFeatAnnotToSeqEntry(), AddGoodPub(), AddGoodSource(), AddLocalIdUserObjects(), AddRefGeneTrackingUserObject(), AddSeqdescToSeqEntryRecursively(), CDRefresher::addSequences(), SequenceTable::addSequences(), AddSource(), AddTitle(), subfuse::CSubmissionCollector::AdjustLocalIds(), AdjustProtFeatForNucProtSet(), CSetGlobalRefGeneStatus::ApplyToCSeq_entry(), CClearKeywords::ApplyToCSeq_entry(), CRemoveBankitComment::ApplyToCSeq_entry(), CRemoveGenomeProjectsDB::ApplyToCSeq_entry(), CRemoveStructuredComment::ApplyToCSeq_entry(), CRemoveSeqAnnot::ApplyToCSeq_entry(), CConvertComment::ApplyToCSeq_entry(), CModifyStructuredComment::ApplyToCSeq_entry(), CRemoveUnverified::ApplyToCSeq_entry(), CRemoveStructuredCommentKeyword::ApplyToCSeq_entry_genbank(), CChangeStructuredCommentKeyword::ApplyToCSeq_entry_user(), CReorderStructuredComment::ApplyToCSeq_entry_user(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), CAttachedHandles::Attach(), BOOST_AUTO_TEST_CASE(), CMacroBioData_SeqSetIter::BuildEditedObject(), ChangeId(), ChangeNucId(), ChangeProtId(), ClearFocus(), CollectDescriptors(), Convert_Seq_entry_Bioseq_set(), Convert_Seq_id_Bioseq_set(), CFeatureTableReader::ConvertNucSetToSet(), CopyBioseqWithType(), CopySeqIdsOfType(), CreateEditorForObject(), CGuiObjectInfoSeq_entry::CreateObject(), CStrainRequest::ExploreStrainsByTaxname(), ExtractBioseq(), FetchSequenceViaHTTP(), CCdsToMatPeptide::FindAnnot(), FindNucInSeqEntry(), sequpd::FixCollidingIDs_Bioseq(), FlattenBioseqSet(), fta_remove_cleanup_user_object(), g_ApplyDescriptors(), CValidError_imp::GatherTentativeName(), CFlatFileGenerator::Generate(), get_parent_seqset(), GetAccessionFromObjects(), CValidError_imp::GetAncestor(), GetBioseqWithType(), CExportTableDlg::GetDesc(), CUnculTaxTool::GetDesc(), CAddFluComments::GetDesc(), CSeq_entryHandler::GetLabel(), CWithdrawSequences::GetNames(), CBioseq_set::GetNucFromNucProtSet(), CFastaIOWrapper::GetNumRead(), CTable2AsnContext::GetOrgName(), CBioseq::GetParentSet(), CBioseq_set::GetParentSet(), CMacroBioData_SeqSetIter::GetScopedObject(), GetSeqLength(), GetSourceDescriptors(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), HasRepairedIDs(), HasSeqIdOfType(), IdFromEntry(), CBioseqEditor::IsEditable(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CReadBlastApp::less_seq(), CTable2AsnContext::MergeWithTemplate(), CDUpdater::modifySeqAlignSeqEntry(), MoveAnnotToTop(), MoveBiomolToTop(), CFeatureTableReader::MoveRegionsToProteins(), CReadBlastApp::NormalizeSeqentry(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), CForeignContaminationScreenReportReader::PostProcess(), CRemoteUpdater::PostProcessPubs(), CTbl2AsnApp::ProcessAlignmentFile(), CPhrapReader::Read(), CFastaReader::ReadAlignedSet(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), UpdateViewer::ReadSequencesFromFile(), CFastaReader::ReadSet(), CDUpdater::reformatBioseq(), RemoveDbxref(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RemoveNcbiCleanupObject(), CCdsToMatPeptide::RemoveProteins(), RemoveTitlesSeqEntry(), RemoveUserObjectType(), ResetOrgname(), RevComp(), CMacroBioData_SeqSetIter::RunDeleteCommand(), CMacroBioData_SeqSetIter::RunEditCommand(), s_CollectCollidingIDs_Entry(), s_CollectPubDescriptorLabels(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CountTopSetSiblings(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetJustNucSeqEntry(), s_GetSourceDescriptors(), s_HasUnprocessedCdregions(), s_IsHtgInSep(), CRemoveSeqFromAlignDlg::SearchSeq_entry(), SetChromosome(), SetCommon(), SetDbxref(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), CNewCleanup_imp::SetGlobalFlags(), SetLineage(), SetMGcode(), SetNucProtSetProductName(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), CTable2AsnContext::SetSeqId(), SetSubSource(), CValidErrorSuppress::SetSuppressedCodes(), SetTaxname(), SetTaxon(), SetTransgenic(), ShowOrgRef(), SimplifySeqEntryForCD(), SortSeqDescr(), CSegregateSetsBase::TakeFromSet(), TrimEntry(), CCmdAddSeqEntry::Unexecute(), CCmdInsertBioseqSet::Unexecute(), CDeflineProcess::UnindexedProcess(), CValidError_imp::Validate(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqParts(), CConversionApp::Write(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CDescPlacementPanel::x_AddToStrings(), CSequenceUpdater::x_AdjustProteinFeature(), CAppendModToOrg::x_ApplyToDescriptors(), CApplyGCode::x_ApplyToDescriptors(), CCountryConflict::x_ApplyToDescriptors(), CCountryFixup::x_ApplyToDescriptors(), CLatLonTool::x_ApplyToDescriptors(), IModifyBiosourceQuals::x_ApplyToDescriptors(), IPubDescEditor::x_ApplyToDescriptors(), IRemovePubs::x_ApplyToDescriptors(), CRemoveUnreviewed::x_ApplyToSeq_entry(), CRemoveDescDlg::x_ApplyToSeq_entry(), CStrainRequest::x_CollectStrainsForRecord(), CDesktopDataBuilder::x_CreateSet(), CPrimeCacheApplication::x_ExtractAndIndex(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CRemoteBlast::x_ExtractQueryIds(), CAsnCacheTestApplication::x_FindAnnotated(), CTaxValidationAndCleanup::x_GatherSources(), SWGSCreateInfo::x_GetProtSet(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), CAgpconvertApplication::x_LoadTemplate(), CFeatTableViewFactory::x_NeedsConversion(), CViewGraphicFactory::x_NeedsConversion(), CBioseq_set_Info::x_ParentAttach(), CStrainSerotypeInfluenza::x_ParseDescriptors(), CCleanupApp::x_ProcessTraditionally(), CNgAlignApp::x_RecurseSeqEntry(), CNewCleanup_imp::x_RemoveDupBioSource(), CNewCleanup_imp::x_RemovePub(), CMacroBioData_SeqSetIter::x_SetDefaultObjectInfo(), CPrimeCacheApplication::x_StripSeqEntry(), CStrainSerotypeInfluenza::x_TestEntryForParsing(), CFormatGuessEx::x_TryFasta(), CSequenceUpdater::x_UpdateProteinID(), CMultiReader::xApplyTemplate(), CFeatureTableReader::xCheckIfNeedConversion(), CFeatureTableReader::xParseCdregions(), CTbl2AsnApp::xProcessOneFile(), seqsubmit_split::CSeqSubSplitter::xTryProcessSeqEntry(), and CRemoteUpdater::xUpdatePubReferences().
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Check if a value has been assigned to Annot data member.
Data member Annot is optional; its type is defined as 'typedef list< CRef< CSeq_annot > > TAnnot'
Definition at line 769 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_set_State.
Referenced by AddFeat(), CDiscrepancyContext::AutofixBioseq_set(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), ChangeId(), ChangeNucId(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), MoveAnnotToTop(), CDiscrepancyContext::PopulateSeqSet(), CReadBlastApp::RemoveProblems(), s_RemoveAnnotsFromEntry(), s_UpdateFeatureIds(), CBioseq_set_Info::sx_ShallowCopy(), TrimEntry(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateGenProdSet(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CNewCleanup_imp::x_CollapseSet(), CAsnCacheTestApplication::x_FindAnnotated(), CSeqMasterIndex::x_InitSeqs(), CNewCleanup_imp::x_MergeAdjacentFeatureTables(), CNewCleanup_imp::x_RemoveEmptyFeatureTables(), CBioseq_set_Info::x_SetObject(), CSplitDataLoader::x_SplitSet(), and seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry().
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Check if a value has been assigned to Class data member.
Data member Class is optional with default eClass_not_set; its type is defined as 'typedef EClass TClass'
Definition at line 605 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_set_State.
Referenced by CTbl2AsnApp::AddAnnots(), AddSeqdescToSeqEntryRecursively(), AddTitle(), CSourceModParser::ApplyAllMods(), CTable2AsnContext::ApplyComments(), CTable2AsnContext::ApplyCreateUpdateDates(), CValidError_bioseqset::CheckForInconsistentBiomols(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CBlobSplitterImpl::CopySkeleton(), CBioseq_set::GetLabel(), CDeflineProcess::IndexedProcess(), CValidError_imp::IsHugeSet(), MoveAnnotToTop(), MoveBiomolToTop(), CSegregateSetsBase::MoveDescrToEntries(), CBioseq_set::NeedsDocsumTitle(), seqsubmit_split::NeedToProcess(), CConvertSetTypeDlg::OnTreebookSelChanged(), CDiscrepancyContext::ParseObject(), CRemoveSet::remove_sets_from_set(), CRemoveSet::RemoveOneSet(), RevComp(), s_CountTopSetSiblings(), s_HasUnprocessedCdregions(), s_IsValidNPSubset(), sApplyDescriptors(), CNewCleanup_imp::SeqsetBC(), CBioseq_set_Base::SetClass(), CBioseq_set_Info::sx_ShallowCopy(), CDeflineProcess::UnindexedProcess(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqParts(), CValidError_bioseqset::ValidateSetElements(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CNewCleanup_imp::x_ChangePopToPhy(), CNewCleanup_imp::x_MovePopPhyMutPub(), CNewCleanup_imp::x_RemoveNestedNucProtSet(), CValidError_bioseqset::x_ValidateSetDescriptors(), CFeatureTableReader::xCheckIfNeedConversion(), and CFeatureTableReader::xMergeCDSFeatures_impl().
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to identify a collection Check if a value has been assigned to Coll data member.
Data member Coll is optional; its type is defined as 'typedef CDbtag TColl'
Definition at line 537 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Coll.
Referenced by CBioseq_set_Base::CanGetColl(), CBlobSplitterImpl::CopySkeleton(), CBioseq_set_Info::sx_ShallowCopy(), and TrimEntry().
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Check if a value has been assigned to Date data member.
Data member Date is optional; its type is defined as 'typedef CDate TDate'
Definition at line 702 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Date.
Referenced by CAutogeneratedCleanup::BasicCleanupBioseqSet(), CBioseq_set_Base::CanGetDate(), CBlobSplitterImpl::CopySkeleton(), CBioseq_set_Info::sx_ShallowCopy(), TrimEntry(), and CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set().
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Check if a value has been assigned to Descr data member.
Data member Descr is optional; its type is defined as 'typedef CSeq_descr TDescr'
Definition at line 723 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Descr.
Referenced by CAutogeneratedCleanup::BasicCleanupBioseqSet(), CBioseq_set_Base::CanGetDescr(), CollectDescriptors(), CBlobSplitterImpl::CopySkeleton(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), FixDupDates(), FixEmblUpdateDates(), fta_remove_cleanup_user_object(), CEditObjectSet::GetEditCommand(), CTable2AsnContext::GetOrgName(), CRemoveSet::MoveDescrToEntries(), CSegregateSetsBase::MoveDescrToEntries(), MoveSourceDescrToTop(), CReadBlastApp::NormalizeSeqentry(), CSequenceEditingEventHandler::SaveDescriptors(), CValidError_bioseqset::SetShouldNotHaveMolInfo(), CValidError_bioseqset::ShouldHaveNoDblink(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), TrimEntry(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidateSetTitle(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_ClearEmptyDescr(), CNewCleanup_imp::x_CollapseSet(), CSeqMasterIndex::x_InitSeqs(), CNewCleanup_imp::x_MoveNpDBlinks(), CNewCleanup_imp::x_MoveNpPub(), CNewCleanup_imp::x_MovePopPhyMutPub(), CNewCleanup_imp::x_RemoveDupBioSource(), CSplitDataLoader::x_SplitSet(), CValidError_bioseqset::x_ValidateSetDescriptors(), and seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry().
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Check if a value has been assigned to Id data member.
Data member Id is optional; its type is defined as 'typedef CObject_id TId'
Definition at line 516 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Id.
Referenced by CBioseq_set_Base::CanGetId(), CBlobSplitterImpl::CopySkeleton(), CBioseq_set_Info::sx_ShallowCopy(), and TrimEntry().
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nesting level Check if a value has been assigned to Level data member.
Data member Level is optional; its type is defined as 'typedef int TLevel'
Definition at line 558 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_set_State.
Referenced by CBioseq_set_Base::CanGetLevel(), CBlobSplitterImpl::CopySkeleton(), CBioseq_set_Base::SetLevel(), CBioseq_set_Info::sx_ShallowCopy(), and TrimEntry().
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Check if a value has been assigned to Release data member.
Data member Release is optional; its type is defined as 'typedef string TRelease'
Definition at line 655 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_set_State.
Referenced by CBioseq_set_Base::CanGetRelease(), CBlobSplitterImpl::CopySkeleton(), CBioseq_set_Base::SetRelease(), CBioseq_set_Info::sx_ShallowCopy(), and TrimEntry().
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Check if a value has been assigned to Seq_set data member.
Data member Seq_set is mandatory; its type is defined as 'typedef list< CRef< CSeq_entry > > TSeq_set'
Definition at line 744 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_set_State.
Referenced by CTbl2AsnApp::AddAnnots(), AddFeatAnnotToSeqEntry(), AddLocalIdUserObjects(), CFeatureTableReader::AddProteins(), AddSeqdescToSeqEntryRecursively(), subfuse::CSubmissionCollector::AdjustLocalIds(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), CConvertSetTypeDlg::ChangeNotify(), CValidError_bioseqset::CheckForImproperlyNestedSets(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), FixDupDates(), FixEmblUpdateDates(), CBioseq_set::GetLabel(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), GetSourceDescriptors(), HasRepairedIDs(), CValidError_bioseqset::IsCDSProductInGPS(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CMagicBlastThread::Main(), CBiosampleChkApp::ProcessSet(), CTLSHandler::ProcessSet(), CCleanup::RemoveNcbiCleanupObject(), CReadBlastApp::RemoveProblems(), RemoveUserObjectType(), CCleanup::RenormalizeNucProtSets(), s_CollectCollidingIDs_Entry(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CountTopSetSiblings(), s_DescriptorPropagateDown(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetJustNucSeqEntry(), s_GetSeqFromSet(), s_GetSourceDescriptors(), s_HasTopSetSiblings(), s_ScanWhilePossibleNPSet(), s_UpdateFeatureIds(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), CSplitCacheApp::TestSplitBioseq(), CCmdInsertBioseqSet::Unexecute(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CValidError_bioseqset::ValidateSetElements(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_CollapseSet(), CCreateGeneModelTask::x_GetCommand(), CNewCleanup_imp::x_MovePopPhyMutPub(), CNewCleanup_imp::x_RemoveDupBioSource(), CNewCleanup_imp::x_RemoveNestedGenBankSet(), CNewCleanup_imp::x_RemoveNestedNucProtSet(), and CBioseq_set_Info::x_SetObject().
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Reset the whole object.
Definition at line 174 of file Bioseq_set_.cpp.
References CBioseq_set_Base::ResetAnnot(), CBioseq_set_Base::ResetClass(), CBioseq_set_Base::ResetColl(), CBioseq_set_Base::ResetDate(), CBioseq_set_Base::ResetDescr(), CBioseq_set_Base::ResetId(), CBioseq_set_Base::ResetLevel(), CBioseq_set_Base::ResetRelease(), and CBioseq_set_Base::ResetSeq_set().
Referenced by CBlobSplitterImpl::CopySkeleton(), and CCleanupApp::x_ProcessTraditionally().
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Reset the whole object.
Definition at line 52 of file Seq_entry_.cpp.
References CSeq_entry_Base::e_not_set, CSeq_entry_Base::m_choice, and CSeq_entry_Base::ResetSelection().
Referenced by CSeq_entry_Base::~CSeq_entry_Base().
void CBioseq_set_Base::ResetAnnot | ( | void | ) |
Reset Annot data member.
Definition at line 168 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Annot, and CBioseq_set_Base::m_set_State.
Referenced by BOOST_AUTO_TEST_CASE(), MoveAnnotToTop(), CCdsToMatPeptide::RemoveFeature(), CReadBlastApp::RemoveProblems(), CBioseq_set_Base::Reset(), s_RemoveAnnotsFromEntry(), CSequenceUpdater::x_PrepareNewEntry(), CNewCleanup_imp::x_RemoveEmptyFeatureTables(), and CPrimeCacheApplication::x_StripSeqEntry().
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Reset Class data member.
Definition at line 617 of file Bioseq_set_.hpp.
References CBioseq_set_Base::eClass_not_set, CBioseq_set_Base::m_Class, and CBioseq_set_Base::m_set_State.
Referenced by CBioseq_set_Base::Reset(), and CBioseq_set_Base::SetDefaultClass().
void CBioseq_set_Base::ResetColl | ( | void | ) |
Reset Coll data member.
Definition at line 105 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Coll.
Referenced by CBioseq_set_Base::Reset().
void CBioseq_set_Base::ResetDate | ( | void | ) |
Reset Date data member.
Definition at line 128 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Date.
Referenced by CBioseq_set_Base::Reset().
void CBioseq_set_Base::ResetDescr | ( | void | ) |
Reset Descr data member.
Definition at line 145 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Descr.
Referenced by BOOST_AUTO_TEST_CASE(), BuildProtBioseqSet(), CEditObjectSet::GetEditCommand(), CTable2AsnContext::MergeSeqDescr(), CRemoveSet::MoveDescrToEntries(), CSegregateSetsBase::MoveDescrToEntries(), CCleanup::RemoveNcbiCleanupObject(), CBioseq_set_Base::Reset(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_ClearEmptyDescr(), CSplitDataLoader::x_SplitSet(), and CPrimeCacheApplication::x_StripSeqEntry().
END_ENUM_INFO void CBioseq_set_Base::ResetId | ( | void | ) |
Reset Id data member.
Definition at line 88 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Id.
Referenced by CBioseq_set_Base::Reset().
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Reset Level data member.
Definition at line 570 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Level, and CBioseq_set_Base::m_set_State.
Referenced by CBioseq_set_Base::Reset().
void CBioseq_set_Base::ResetRelease | ( | void | ) |
Reset Release data member.
Definition at line 122 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Release, and CBioseq_set_Base::m_set_State.
Referenced by CBioseq_set_Base::Reset().
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Reset the selection (set it to e_not_set).
Definition at line 58 of file Seq_entry_.cpp.
References CSeq_entry_Base::e_not_set, CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CSeq_entry_Base::m_choice, and CSeq_entry_Base::m_object.
Referenced by CSeq_entry_Base::Reset(), CSeq_entry_Base::SetSeq(), and CSeq_entry_Base::SetSet().
void CBioseq_set_Base::ResetSeq_set | ( | void | ) |
Reset Seq_set data member.
Definition at line 162 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Seq_set, and CBioseq_set_Base::m_set_State.
Referenced by CReorderSequencesDlg::PopulateSet(), and CBioseq_set_Base::Reset().
void CSeq_entry_Base::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CSeq_entry_Base::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
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Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
Referenced by CBasicFastaWrapper::ReadFile(), CSeq_entry_Base::SetSeq(), and CSeq_entry_Base::SetSet().
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Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 92 of file Seq_entry_.cpp.
References CSeq_entry_Base::sm_SelectionNames.
Referenced by CSeq_entry::GetAnnot(), CSeq_entry::GetDescr(), CSeq_entry::SetAnnot(), and CSeq_entry::SetDescr().
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Assign a value to Annot data member.
Definition at line 787 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Annot, and CBioseq_set_Base::m_set_State.
Referenced by CObjectManager::AcquireSharedSeq_annot(), AddFeat(), CAttachedHandles::Attach(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildGoodEcoSetWithAlign(), BuildProtBioseqSet(), ChangeId(), ChangeNucId(), Check3Extend(), Check5Extend(), Check5Policy(), CheckFeatSeqLoc(), CheckGene(), CheckPropagatedCDSLocation(), Convert_Seq_annot_Seq_entry(), CBlobSplitterImpl::CopySkeleton(), CreateBioseqsAndAlign(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAnnotationASN1::CImplementationData::DumpEvidence(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), GetCDSFromGoodNucProtSet(), CSNPDbSeqIterator::GetEntry(), GetGoodSeqEntryWithFeatureIds(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CBamRefSeqInfo::LoadMainEntry(), CCSRAFileInfo::LoadReadsBlob(), MoveAnnotToTop(), CBam2GraphApp::ProcessFile(), CBam2GraphApp::ProcessSrz(), CGlimmerReader::Read(), CConversionApp::Read(), CFastaReaderEx::ReadAlignedSet(), CFastaReader::ReadAlignedSet(), CFeature_table_reader::ReadSequinFeatureTables(), CReadBlastApp::RemoveProblems(), ReplaceWellknownSeqs(), CAnnotationASN1::CImplementationData::ResetASN1(), RevComp(), s_AddCDS(), s_UpdateFeatureIds(), TestFeatInsideGap(), TrimEntry(), TruncateTransSplicedCDSForExtension(), SWGSCreateInfo::x_AddFeaturesDirect(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CPhrap_Contig::x_CreateAlignAll(), CPhrap_Contig::x_CreateAlignOptimized(), CPhrap_Contig::x_CreateAlignPairs(), CID2SNPProcessor_Impl::x_LoadBlob(), CScope_Impl::x_MakeDummyTSE(), CNewCleanup_imp::x_MergeAdjacentFeatureTables(), CGFFReader::x_PlaceAlignment(), CGFFReader::x_PlaceFeature(), CNewCleanup_imp::x_RemoveEmptyFeatureTables(), CSplitDataLoader::x_SplitSet(), and CFeatureTableReader::xParseCdregions().
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Assign a value to Class data member.
value | Value to assign |
Definition at line 636 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Class, CBioseq_set_Base::m_set_State, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildBioSegHeader(), BuildGenProdSetWithBigProduct(), BuildGoodEcoSet(), BuildGoodGenProdSet(), BuildGoodSegSet(), seqsubmit_split::CSeqEntryHelper::BuildObject(), BuildProtBioseqSet(), BuildSmallGenomeSet(), CConvertSetTypeDlg::ChangeNotify(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CFeatureTableReader::ConvertNucSetToSet(), CBlobSplitterImpl::CopySkeleton(), CPhrap_Contig::CreateContig(), CCmdInsertBioseqSet::Execute(), CEditObjectSet::GetEditCommand(), CSraRun::GetSpotEntry(), MakeBioseqSet(), CInfluenzaSet::MakeSet(), s_MakeGroupsForUniqueValues(), SeqEntryFromSeqSubmit(), CNewCleanup_imp::SeqsetBC(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), TrimEntry(), CNewCleanup_imp::x_ChangePopToPhy(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), SWGSCreateInfo::x_GetProtSet(), CGC_Assembly_Parser::x_InitSeq_entry(), CCleanupApp::x_ProcessHugeFileBlob(), CFeatureTableReader::xConvertSeqIntoSeqSet(), and seqsubmit_split::CSeqSubSplitter::xWrapSeqEntries().
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Assign a value to Class data member.
Definition at line 643 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetClass(), CBioseq_set_Base::m_Class, CBioseq_set_Base::m_set_State, and CSerialObject::UnassignedByte().
void CBioseq_set_Base::SetColl | ( | CBioseq_set_Base::TColl & | value | ) |
Assign a value to Coll data member.
value | Reference to value. |
Definition at line 110 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Coll, and rapidjson::value.
Referenced by CBlobSplitterImpl::CopySkeleton(), and TrimEntry().
CBioseq_set_Base::TColl & CBioseq_set_Base::SetColl | ( | void | ) |
Assign a value to Coll data member.
Definition at line 115 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Coll.
void CBioseq_set_Base::SetDate | ( | CBioseq_set_Base::TDate & | value | ) |
Assign a value to Date data member.
value | Reference to value. |
Definition at line 133 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Date, and rapidjson::value.
Referenced by CAutogeneratedCleanup::BasicCleanupBioseqSet(), CBlobSplitterImpl::CopySkeleton(), MakeBioseqSet(), TrimEntry(), and CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set().
CBioseq_set_Base::TDate & CBioseq_set_Base::SetDate | ( | void | ) |
Assign a value to Date data member.
Definition at line 138 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Date.
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Assign default value to Class data member.
Definition at line 624 of file Bioseq_set_.hpp.
References CBioseq_set_Base::ResetClass().
void CBioseq_set_Base::SetDescr | ( | CBioseq_set_Base::TDescr & | value | ) |
Assign a value to Descr data member.
value | Reference to value. |
Definition at line 150 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Descr, and rapidjson::value.
Referenced by AddGoodPub(), AddGoodSource(), AddRefGeneTrackingUserObject(), AddSource(), AddTitle(), CSegregateSetsBase::AddUserObject(), CTable2AsnContext::ApplyComments(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), BOOST_AUTO_TEST_CASE(), BuildBioSegHeader(), BuildGoodEcoSet(), BuildProtBioseqSet(), ClearFocus(), CBlobSplitterImpl::CopySkeleton(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), FixDupDates(), FixEmblUpdateDates(), fta_get_user_object(), fta_remove_cleanup_user_object(), CEditObjectSet::GetEditCommand(), MoveSourceDescrToTop(), CReadBlastApp::NormalizeSeqentry(), RemoveDbxref(), ResetOrgname(), sApplyDescriptors(), SetChromosome(), SetCommon(), SetDbxref(), CSeq_entry::SetDescr(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), SetLineage(), SetMGcode(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), SetSubSource(), SetTaxname(), SetTaxon(), SetTransgenic(), TrimEntry(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CPhrapReader::x_CreateDesc(), CNewCleanup_imp::x_MoveNpPub(), CNewCleanup_imp::x_MovePopPhyMutPub(), CGFFReader::x_ParseDateComment(), CSplitDataLoader::x_SplitSet(), and seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry().
CBioseq_set_Base::TDescr & CBioseq_set_Base::SetDescr | ( | void | ) |
Assign a value to Descr data member.
Definition at line 155 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Descr.
void CBioseq_set_Base::SetId | ( | CBioseq_set_Base::TId & | value | ) |
Assign a value to Id data member.
value | Reference to value. |
Definition at line 93 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Id, and rapidjson::value.
Referenced by CBlobSplitterImpl::CopySkeleton(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CBamRefSeqInfo::LoadMainEntry(), CBamRefSeqInfo::LoadMainSplit(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), TrimEntry(), SWGSCreateInfo::x_GetProtSet(), CID2SNPProcessor_Impl::x_LoadBlob(), and CSplitDataLoader::x_SplitSet().
CBioseq_set_Base::TId & CBioseq_set_Base::SetId | ( | void | ) |
Assign a value to Id data member.
Definition at line 98 of file Bioseq_set_.cpp.
References CBioseq_set_Base::m_Id.
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Assign a value to Level data member.
value | Value to assign |
Definition at line 586 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Level, CBioseq_set_Base::m_set_State, and rapidjson::value.
Referenced by CBlobSplitterImpl::CopySkeleton(), CPhrap_Contig::CreateContig(), CSraRun::GetSpotEntry(), TrimEntry(), CPhrapReader::x_ConvertContig(), and CGC_Assembly_Parser::x_InitSeq_entry().
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Assign a value to Level data member.
Definition at line 593 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetLevel(), CBioseq_set_Base::m_Level, CBioseq_set_Base::m_set_State, and CSerialObject::UnassignedByte().
Assign a value to Release data member.
value | Value to assign |
Definition at line 676 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Release, CBioseq_set_Base::m_set_State, and rapidjson::value.
Referenced by CBlobSplitterImpl::CopySkeleton(), MakeBioseqSet(), and TrimEntry().
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Definition at line 683 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Release, CBioseq_set_Base::m_set_State, and rapidjson::value.
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Assign a value to Release data member.
Definition at line 690 of file Bioseq_set_.hpp.
References CBioseq_set_Base::IsSetRelease(), CBioseq_set_Base::m_Release, CBioseq_set_Base::m_set_State, and CSerialObject::UnassignedString().
void CSeq_entry_Base::SetSeq | ( | CSeq_entry_Base::TSeq & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 114 of file Seq_entry_.cpp.
References CObject::AddReference(), CSeq_entry_Base::e_Seq, CSeq_entry_Base::m_choice, CSeq_entry_Base::m_object, CSeq_entry_Base::ResetSelection(), and rapidjson::value.
CSeq_entry_Base::TSeq & CSeq_entry_Base::SetSeq | ( | void | ) |
Select the variant.
Definition at line 108 of file Seq_entry_.cpp.
References CSeq_entry_Base::e_Seq, eDoNotResetVariant, CSeq_entry_Base::m_object, and CSeq_entry_Base::Select().
Referenced by CObjectManager::AcquireSharedBioseq(), CTbl2AsnApp::AddAnnots(), AddFeat(), AddFeatAnnotToSeqEntry(), AddGenbankKeyword(), AddGoodImpFeat(), AddGoodPub(), AddGoodSource(), AddLocalIdUserObjects(), CObjectLoadingTask::AddObjects(), CGBProjectHelper::AddProjectItemsFromRID(), CCleanup::AddProtein(), AddProtRefSeqEntry(), AddRefGeneTrackingUserObject(), AddSentinelRNASeq(), AddSeqdescToSeqEntryRecursively(), CDRefresher::addSequences(), SequenceTable::addSequences(), AddSource(), AddTitle(), AddToDeltaSeq(), AddTpaAssemblyUserObject(), AdjustProtFeatForNucProtSet(), AgpRead(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CAttachedHandles::Attach(), CAutogeneratedCleanup::BasicCleanupSeqEntry(), CDUpdater::blast(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildBigGoodNucProtSet(), BuildBioSegHeader(), BuildGapFuzz100DeltaSeq(), BuildGenProdSetWithBigProduct(), BuildGoodDeltaSeq(), BuildGoodGenProdSet(), BuildGoodNucProtSet(), BuildGoodProtSeq(), BuildGoodSegSet(), BuildGoodSeq(), BuildGoodSpliceNucProtSet(), BuildNucProtSet(), BuildSegSetPart(), BuildSequence(), ChangeGoodNucProtSetIdToGenbankName(), ChangeId(), ChangeNucId(), ChangeNucProtSetNucId(), ChangeNucProtSetProteinId(), ChangeProtId(), CheckLocalId(), CkInitMetSP(), CkNonTerSP(), ClearFocus(), Convert_Bioseq_Seq_entry(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CGapsEditor::ConvertNs2Gaps(), CCopyHook_Bioseq::CopyObject(), CBlobSplitterImpl::CopySkeleton(), CCreateProteinId::create_protein_ids(), CAlnVecMultiDataSource::CreateConsensus(), CAlnVec::CreateConsensus(), CPhrap_Contig::CreateContig(), CreateMimeFromBiostruc(), CPhrap_Read::CreateRead(), CMytestApplication::DoProcessFeatureGeneOverlap(), CDiscrepancyContext::Extend(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), FetchSequenceViaHTTP(), CFeatureTableReader::FindOpenReadingFrame(), StructureSet::FindOrCreateSequence(), CDUpdater::findSeq(), SequenceTable::findSequence(), fta_get_user_object(), fta_remove_cleanup_user_object(), CFlatFileGenerator::Generate(), GetBioseqWithType(), GetCDSFromGenProdSet(), CModifySeqId::GetCommand(), GetGoodSeqEntryWithFeatureIds(), CWGSDb_Impl::GetMasterSeq_entry(), GetmRNAFromGenProdSet(), CMaskBDBReader::GetNextSequence(), CDUpdater::GetOneBioseqFromSeqEntry(), GetProtFeatFromGoodNucProtSet(), CMytestApplication::GetSeqEntry(), CSeqSetPresenter::GetSeqEntry(), GetSPAnnot(), CSraRun::GetSpotEntry(), TaxTreeData::GetTaxIDForSequence(), PssmMaker::getTrunctMaster(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), IdFromEntry(), CwxDemoAlignTableFrame::LoadAccession(), CwxDemoFeatureTableFrame::LoadAccession(), CTSE_Default_Assigner::LoadChunkBioseqs(), CwxDemoAlignTableFrame::LoadFile(), CwxDemoFeatureTableFrame::LoadFile(), CFastaObjectLoader::LoadFromStream(), CAsnObjectLoader::LoadFromStream(), CCSRAFileInfo::LoadReadsBlob(), CCSRARefSeqInfo::LoadRefSeqMainEntry(), CMultiReader::LoadTemplate(), CMakeCdrProds::MakeCdrProds(), MakeEntryForDeltaConversion(), MakeNucProtSet3Partial(), MakeProteinForGoodNucProtSet(), MakeProteinForNucProtSet(), CBam2Seq_graph::MakeSeq_entry(), CCdsToMatPeptide::MergeConvert(), CTable2AsnContext::MergeSeqDescr(), CDUpdater::modifySeqAlignSeqEntry(), CSequenceIStreamBlastDB::next(), CReadBlastApp::NormalizeSeqentry(), CSequesterSets::OnAccept(), CDesktopViewContext::OnPasteSelection(), CPrimeCacheApplication::CCacheBioseq::operator()(), CAgpConverter::OutputBioseqs(), CSeq_entry::Parentize(), CSeq_entry::ParentizeOneLevel(), CRemoteUpdater::PostProcessPubs(), PSSMWrapper::PSSMWrapper(), CGlimmerReader::Read(), CConversionApp::Read(), CHugeFileProcess::Read(), CFastaReaderEx::ReadDeltaFasta(), CBlastInputReader::ReadOneSeq(), CFastaReader::ReadOneSeq(), CGff2Reader::ReadSeqEntry(), UpdateViewer::ReadSequencesFromFile(), CFeature_table_reader::ReadSequinFeatureTables(), CCachedSequence::RegisterIds(), RemoveDbxref(), RemoveDeltaSeqGaps(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RemoveNcbiCleanupObject(), CReadBlastApp::RemoveProblems(), RemoveUserObjectType(), ReplaceWellknownSeqs(), ResetOrgname(), RetranslateCdsForNucProtSet(), RevComp(), CLocalFinderApp::Run(), CAgpconvertApplication::Run(), s_AddSeqDataToPssm(), s_AddSeqTitleToPssm(), s_ArePrimersUnique(), s_CollectCollidingIDs_Entry(), s_CollidedIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_FastaStringToBioseq(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetQueryBioseq(), s_MakeNewMasterSeq(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(), s_QueryVectorToBioseqSet(), s_RemoveAnnotsFromEntry(), s_SetSeqdescUser(), s_TSeqLocVectorToBioseqSet(), s_UpdateFeatureIds(), SeqEntryFromSeqSubmit(), CSeq_entry::SetAnnot(), SetBiomol(), SetChromosome(), SetCommon(), SetCompleteness(), SetDbxref(), CSeq_entry::SetDescr(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), SetLineage(), SetMGcode(), SetNucProtSetProductName(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), CTable2AsnContext::SetSeqId(), SetSubSource(), SetTaxname(), SetTaxon(), SetTech(), SetTitle(), SetTransgenic(), CValidError_imp::Setup(), SimplifySeqEntryForCD(), SPFeatProtRef(), CCachedSequence::SplitSeqData(), SrchSegDescr(), TestCircularTopology(), TestFeatInsideGap(), TestNewAccessionOnNuc(), TestNewAccessionOnStandaloneProt(), TestOneGapSeq(), TestOneGeneralSeqId(), TestOneLongGeneral(), TestOneMiscPartial(), TestOneOtherAcc(), TestOneReplicon(), TestOneStrain(), TestOneStrainNew(), TestStartGapSeg(), TranslateCDSCommand(), TryMiscWithNs(), UnpackSeqEntry(), CDUpdater::update(), CGC_Assembly_Parser::x_AddBioseq(), CCachedSequence::x_AddFullSeq_data(), SWGSCreateInfo::x_AddProducts(), CSequenceUpdater::x_AdjustProteinFeature(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E(), x_BioseqSetFromBioseq(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), CPssmEngine::x_CreatePssmFromMsa(), CImportFeatTable::x_DoImportCDS(), CAgpToSeqEntry::x_FinishedBioseq(), CSequenceUpdater::x_FixIDInNewEntry(), CBamAlignIterator::x_GetMatchEntry(), CCSraAlignIterator::x_GetMatchEntry(), SWGSCreateInfo::x_GetProtSet(), CEditObjectSeq_feat::x_HandleCdsProduct(), CSeqMasterIndex::x_Initialize(), CAgpConverter::x_InitializeAndCheckCopyOfTemplate(), CAgpConverter::x_InitializeCopyOfTemplate(), CBuffer_DataLoader::x_LoadData(), CSplitDataLoader::x_LoadData(), CAgpconvertApplication::x_LoadTemplate(), CScope_Impl::x_MakeDummyTSE(), CNewCleanup_imp::x_MoveNpDBlinks(), CGFFReader::x_PlaceSeq(), CSequenceUpdater::x_PrepareNewEntry(), CPrimeCacheApplication::x_Process_Fasta(), CCleanupApp::x_ProcessTraditionally(), CShortReadFastaInputSource::x_ReadFastaOneSeq(), CGFFReader::x_ReadFastaSequences(), CShortReadFastaInputSource::x_ReadFastc(), CShortReadFastaInputSource::x_ReadFastqOneSeq(), CGapStatsApplication::x_ReadFileOrAccn(), CASN1InputSourceOMF::x_ReadFromSingleFile(), CASN1InputSourceOMF::x_ReadFromTwoFiles(), CSraInputSource::x_ReadOneSeq(), CSraInputSource::x_ReadPairs(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CNewCleanup_imp::x_RemovePub(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), CSequenceUpdater::x_RetranslateOldCDSProduct(), CNetBlastSubmittingJob::x_Run(), CBioseq_set_Info::x_SetChunkBioseqs2(), CAgpConverter::x_SetCreateAndUpdateDatesToToday(), CCDSTranslationPanel::x_SetLocationForProtein(), CSeq_entry_Info::x_SetObject(), CCDSTranslationPanel::x_SetProtein(), CPrimeCacheApplication::x_StripSeqEntry(), CSequenceUpdater::x_UpdateProteinID(), CFeatureTableReader::xAddProteinToSeqEntry(), CFeatureTableReader::xConvertSeqIntoSeqSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatTableEdit::xGenerate_mRNA_Product(), CMultiReader::xReadASN1Text(), and CFeatureTableReader::xTranslateProtein().
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Assign a value to Seq_set data member.
Definition at line 762 of file Bioseq_set_.hpp.
References CBioseq_set_Base::m_Seq_set, and CBioseq_set_Base::m_set_State.
Referenced by CObjectManager::AcquireSharedSeq_annot(), CTbl2AsnApp::AddAnnots(), AddCdregionToSmallGenomeSet(), AddCDSAndProtForBigGoodNucProtSet(), AddChromosomeNoLocation(), AddFeatAnnotToSeqEntry(), AddLocalIdUserObjects(), CGBProjectHelper::AddProjectItemsFromRID(), AddSeqdescToSeqEntryRecursively(), CCdCore::AddSequence(), CDRefresher::addSequences(), SequenceTable::addSequences(), AddTitle(), subfuse::CSubmissionCollector::AdjustLocalIds(), AdjustProtFeatForNucProtSet(), AgpRead(), CReadBlastApp::AnalyzeSeqs(), CReadBlastApp::AnalyzeSeqsViaBioseqs(), CTable2AsnContext::ApplyCreateUpdateDates(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildBioSegHeader(), BuildGenProdSetWithBigProduct(), BuildGoodEcoSet(), BuildGoodEcoSetWithAlign(), BuildGoodGenProdSet(), BuildGoodSegSet(), BuildGoodSpliceNucProtSet(), BuildProtBioseqSet(), BuildSmallGenomeSet(), ChangeId(), CConvertSetTypeDlg::ChangeNotify(), ChangeNucId(), ChangeProtId(), Check3Policy(), CCdCore::Clear(), Convert_Seq_annot_Seq_entry(), Convert_Seq_entry_Bioseq_set(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CGapsEditor::ConvertNs2Gaps(), CFeatureTableReader::ConvertNucSetToSet(), CBlobSplitterImpl::CopySkeleton(), CreateBioseqsAndAlign(), CPhrap_Contig::CreateContig(), CreateMimeFromBiostruc(), CMytestApplication::DoProcessFeatureGeneOverlap(), CCdCore::EraseSequence(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), FetchSequenceViaHTTP(), CFeatureTableReader::FindOpenReadingFrame(), FixDupDates(), FixEmblUpdateDates(), get_parent_seqset(), CCdCore::GetBioseqForIndex(), GetBioseqWithType(), CCDDDataLoader_Impl::GetBlobBySeq_ids(), CSNPDbSeqIterator::GetEntry(), GetGenomicFromGenProdSet(), GetGoodSeqEntryWithFeatureIds(), seqsubmit_split::CSeqEntryHelper::GetListOfEntries(), CBlastInputOMF::GetNextSeqBatch(), GetNucleotideSequenceFromGoodNucProtSet(), GetNucProtSetFromGenProdSet(), GetProteinSequenceFromGoodNucProtSet(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CSraRun::GetSpotEntry(), IdFromEntry(), CCdFromFasta::ImportAlignmentData(), CFastaObjectLoader::LoadFromStream(), CTextAlignObjectLoader::LoadFromStream(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CCSRAFileInfo::LoadReadsBlob(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), MakeBioseqSet(), CMakeCdrProds::MakeCdrProds(), MakeMultiSeqCDS(), MakeNucProtSet3Partial(), CCdsToMatPeptide::MergeConvert(), CTable2AsnContext::MergeWithTemplate(), MoveAnnotToTop(), MoveBiomolToTop(), CReadBlastApp::NormalizeSeqentry(), OneTerminalTranslationExceptionTest(), CWithdrawSequences::PopulateSet(), CReorderSequencesDlg::PopulateSet(), CSegregateSetsBase::PopulateSet(), CForeignContaminationScreenReportReader::PostProcess(), CRemoteUpdater::PostProcessPubs(), CBam2GraphApp::ProcessFile(), CBam2GraphApp::ProcessSrz(), CGlimmerReader::Read(), CConversionApp::Read(), CBasicFastaWrapper::ReadFile(), CGff2Reader::ReadSeqEntry(), UpdateViewer::ReadSequencesFromFile(), CFastaReader::ReadSet(), CCleanup::RemoveNcbiCleanupObject(), CRemoveSet::RemoveOneSet(), CReadBlastApp::RemoveProblems(), RemoveUserObjectType(), ReplaceWellknownSeqs(), CAnnotationASN1::CImplementationData::ResetASN1(), RevComp(), s_AddCDS(), s_CollectCollidingIDs_Entry(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(), s_QueryVectorToBioseqSet(), s_RemoveAnnotsFromEntry(), s_TSeqLocVectorToBioseqSet(), s_UpdateFeatureIds(), SeqEntryFromSeqSubmit(), SetNucProtSetProductName(), CTable2AsnContext::SetSeqId(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), SimplifySeqEntryForCD(), SortSeqDescr(), CReadBlastApp::SortSeqs(), CSegregateSetsBase::TakeFromSet(), TestCollidingAccessionFixes(), TestFeatInsideGap(), TestGoodNucId(), TrimEntry(), TruncateTransSplicedCDSForExtension(), CConversionApp::Write(), CGC_Assembly_Parser::x_AddBioseq(), SWGSCreateInfo::x_AddProducts(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), x_BioseqSetFromBioseq(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CPhrapReader::x_ConvertContig(), x_CreateEmptyLocalCDDEntry(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CSequenceUpdater::x_FixIDInNewEntry(), CCreateGeneModelTask::x_GetCommand(), CBamAlignIterator::x_GetMatchEntry(), SWGSCreateInfo::x_GetProtSet(), CGC_Assembly_Parser::x_InitSeq_entry(), CID2SNPProcessor_Impl::x_LoadBlob(), CBamRefSeqInfo::x_LoadRangesEstimated(), CScope_Impl::x_MakeDummyTSE(), CNewCleanup_imp::x_MovePopPhyMutPub(), CBioseq_set_Info::x_ParentAttach(), CGFFReader::x_PlaceSeq(), CSequenceUpdater::x_PrepareNewEntry(), CCleanupApp::x_ProcessHugeFileBlob(), CShortReadFastaInputSource::x_ReadFastaOrFastq(), CGFFReader::x_ReadFastaSequences(), CShortReadFastaInputSource::x_ReadFastc(), CASN1InputSourceOMF::x_ReadFromSingleFile(), CASN1InputSourceOMF::x_ReadFromTwoFiles(), CShortReadFastaInputSource::x_ReadFromTwoFiles(), CSraInputSource::x_ReadOneSeq(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CPsiBl2SeqTestFixture::x_ReadSeqEntriesFromFile(), CPsiBlastTestFixture::x_ReadSeqEntriesFromFile(), CFastaReader::x_ReadSeqsToAlign(), CNewCleanup_imp::x_RemoveDupBioSource(), CNetBlastSubmittingJob::x_Run(), CPSGS_CDDProcessor::x_SendAnnot(), CBioseq_set_Info::x_SetObject(), CSplitDataLoader::x_SplitSet(), CPrimeCacheApplication::x_StripSeqEntry(), CMultiReader::xApplyTemplate(), CFeatureTableReader::xConvertSeqIntoSeqSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), CFeatureTableReader::xParseCdregions(), CMultiReader::xReadASN1Text(), CRemoteUpdater::xUpdatePubReferences(), and seqsubmit_split::CSeqSubSplitter::xWrapSeqEntries().
void CSeq_entry_Base::SetSet | ( | CSeq_entry_Base::TSet & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 136 of file Seq_entry_.cpp.
References CObject::AddReference(), CSeq_entry_Base::e_Set, CSeq_entry_Base::m_choice, CSeq_entry_Base::m_object, CSeq_entry_Base::ResetSelection(), and rapidjson::value.
CSeq_entry_Base::TSet & CSeq_entry_Base::SetSet | ( | void | ) |
Select the variant.
Definition at line 130 of file Seq_entry_.cpp.
References CSeq_entry_Base::e_Set, eDoNotResetVariant, CSeq_entry_Base::m_object, and CSeq_entry_Base::Select().
Referenced by CObjectManager::AcquireSharedSeq_annot(), CTbl2AsnApp::AddAnnots(), AddCdregionToSmallGenomeSet(), AddCDSAndProtForBigGoodNucProtSet(), AddChromosomeNoLocation(), AddFeat(), AddFeatAnnotToSeqEntry(), AddGoodPub(), AddGoodSource(), AddLocalIdUserObjects(), CAnnotationASN1::CImplementationData::AddModel(), CObjectLoadingTask::AddObjects(), AddRefGeneTrackingUserObject(), AddSeqdescToSeqEntryRecursively(), CCdCore::AddSequence(), CDRefresher::addSequences(), SequenceTable::addSequences(), AddSource(), AddTitle(), subfuse::CSubmissionCollector::AdjustLocalIds(), AdjustProtFeatForNucProtSet(), CReadBlastApp::AnalyzeSeqs(), CReadBlastApp::AnalyzeSeqsViaBioseqs(), CTable2AsnContext::ApplyCreateUpdateDates(), CAttachedHandles::Attach(), CAutogeneratedCleanup::BasicCleanupSeqEntry(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildBigGoodNucProtSet(), BuildBioSegHeader(), BuildGenProdSetWithBigProduct(), BuildGoodEcoSet(), BuildGoodEcoSetWithAlign(), BuildGoodGenProdSet(), BuildGoodNucProtSet(), BuildGoodSegSet(), BuildGoodSpliceNucProtSet(), BuildNucProtSet(), seqsubmit_split::CSeqEntryHelper::BuildObject(), BuildProtBioseqSet(), BuildSmallGenomeSet(), ChangeId(), ChangeNucId(), ChangeProtId(), Check3Extend(), Check3Policy(), Check5Extend(), Check5Policy(), CheckPropagatedCDSLocation(), CCdCore::Clear(), ClearFocus(), Convert_Bioseq_set_Seq_entry(), Convert_Seq_annot_Seq_entry(), CGapsEditor::ConvertNs2Gaps(), CFeatureTableReader::ConvertNucSetToSet(), CCopyHook_Bioseq_set::CopyObject(), CBlobSplitterImpl::CopySkeleton(), CreateBioseqsAndAlign(), CPhrap_Contig::CreateContig(), CreateMimeFromBiostruc(), CAnnotationASN1::CImplementationData::CreateModelProducts(), CSeqEntrySource::CSeqEntrySource(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAnnotationASN1::CImplementationData::DumpEvidence(), CCdCore::EraseSequence(), CCmdInsertBioseqSet::Execute(), CGBFlatFileObjectLoader::Execute(), CDiscrepancyContext::Extend(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), FetchSequenceViaHTTP(), CCdsToMatPeptide::FindAnnot(), CFeatureTableReader::FindOpenReadingFrame(), fta_get_user_object(), fta_remove_cleanup_user_object(), g_ApplyDescriptors(), CFlatFileGenerator::Generate(), get_parent_seqset(), CCdCore::GetBioseqForIndex(), GetBioseqWithType(), CCDDDataLoader_Impl::GetBlobBySeq_ids(), GetCDSFromGoodNucProtSet(), CSegregateSets::GetCommand(), CWithdrawSequences::GetCommand(), CSNPDbSeqIterator::GetEntry(), GetGenomicFromGenProdSet(), GetGoodSeqEntryWithFeatureIds(), seqsubmit_split::CSeqEntryHelper::GetListOfEntries(), GetNucleotideSequenceFromGoodNucProtSet(), GetNucProtSetFromGenProdSet(), GetProteinSequenceFromGoodNucProtSet(), CMytestApplication::GetSeqEntry(), CSeqSetPresenter::GetSeqEntry(), CSraRun::GetSpotEntry(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), IdFromEntry(), CCdFromFasta::ImportAlignmentData(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CFastaObjectLoader::LoadFromStream(), CAsnObjectLoader::LoadFromStream(), CTextAlignObjectLoader::LoadFromStream(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CBamRefSeqInfo::LoadMainEntry(), CBamRefSeqInfo::LoadMainSplit(), CCSRAFileInfo::LoadReadsBlob(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), MakeMultiSeqCDS(), MakeNucProtSet3Partial(), CInfluenzaSet::MakeSet(), CCdsToMatPeptide::MergeConvert(), CTable2AsnContext::MergeSeqDescr(), CTable2AsnContext::MergeWithTemplate(), MoveAnnotToTop(), MoveBiomolToTop(), CFeatureTableReader::MoveRegionsToProteins(), MoveSourceDescrToTop(), CReadBlastApp::NormalizeSeqentry(), CAsn2FastaApp::ObtainSeqEntryFromBioseqSet(), CAsn2FlatApp::ObtainSeqEntryFromBioseqSet(), CSequesterSets::OnAccept(), OneTerminalTranslationExceptionTest(), CDesktopViewContext::OnPasteSelection(), CSeq_entry::Parentize(), CSeq_entry::ParentizeOneLevel(), CSegregateSetsBase::PopulateSet(), CForeignContaminationScreenReportReader::PostProcess(), CRemoteUpdater::PostProcessPubs(), CBam2GraphApp::ProcessFile(), CBam2GraphApp::ProcessSrz(), CGlimmerReader::Read(), CConversionApp::Read(), CPhrapReader::Read(), CFastaReaderEx::ReadAlignedSet(), CFastaReader::ReadAlignedSet(), CBasicFastaWrapper::ReadFile(), CGff2Reader::ReadSeqEntry(), UpdateViewer::ReadSequencesFromFile(), CFeature_table_reader::ReadSequinFeatureTables(), CFastaReader::ReadSet(), RemoveDbxref(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RemoveNcbiCleanupObject(), CReadBlastApp::RemoveProblems(), CCdsToMatPeptide::RemoveProteins(), RemoveUserObjectType(), ReplaceWellknownSeqs(), CAnnotationASN1::CImplementationData::ResetASN1(), ResetOrgname(), RevComp(), s_AddCDS(), s_CollectCollidingIDs_Entry(), s_CollidedIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_MakeGroupsForUniqueValues(), s_MoveProteinSpecificFeats(), s_RemoveAnnotsFromEntry(), s_UpdateFeatureIds(), SeqEntryFromSeqSubmit(), CSeq_entry::SetAnnot(), SetChromosome(), SetCommon(), SetDbxref(), CSeq_entry::SetDescr(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), SetLineage(), SetMGcode(), SetNucProtSetProductName(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), CTable2AsnContext::SetSeqId(), SetSubSource(), SetTaxname(), SetTaxon(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), SetTransgenic(), SimplifySeqEntryForCD(), SortSeqDescr(), CReadBlastApp::SortSeqs(), sUpdateCase(), TestCollidingAccessionFixes(), TestFeatInsideGap(), TestGoodNucId(), TrimEntry(), TruncateTransSplicedCDSForExtension(), UnpackSeqEntry(), CGC_Assembly_Parser::x_AddBioseq(), SWGSCreateInfo::x_AddProducts(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E(), CPhrapReader::x_ConvertContig(), x_CreateEmptyLocalCDDEntry(), CSequenceUpdater::x_FixIDInNewEntry(), CCreateGeneModelTask::x_GetCommand(), CBamAlignIterator::x_GetMatchEntry(), SWGSCreateInfo::x_GetProtSet(), CSeqMasterIndex::x_Initialize(), CGC_Assembly_Parser::x_InitSeq_entry(), CSplitDataLoader::x_LoadData(), CBamRefSeqInfo::x_LoadRangesEstimated(), CScope_Impl::x_MakeDummyTSE(), CBioseq_set_Info::x_ParentAttach(), CGFFReader::x_ParseDateComment(), CGFFReader::x_PlaceAlignment(), CGFFReader::x_PlaceFeature(), CGFFReader::x_PlaceSeq(), CSequenceUpdater::x_PrepareNewEntry(), CCleanupApp::x_ProcessHugeFileBlob(), CCleanupApp::x_ProcessTraditionally(), CGFFReader::x_ReadFastaSequences(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CPsiBl2SeqTestFixture::x_ReadSeqEntriesFromFile(), CPsiBlastTestFixture::x_ReadSeqEntriesFromFile(), CFastaReader::x_ReadSeqsToAlign(), CNewCleanup_imp::x_RemoveDupBioSource(), CNewCleanup_imp::x_RemovePub(), CPSGS_CDDProcessor::x_SendAnnot(), CSeq_entry_Info::x_SetObject(), CPrimeCacheApplication::x_StripSeqEntry(), CMultiReader::xApplyTemplate(), CFeatureTableReader::xConvertSeqIntoSeqSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), CFeatureTableReader::xParseCdregions(), CAnnotWriterApp::xProcessInputObject(), CMultiReader::xReadASN1Text(), CRemoteUpdater::xUpdatePubReferences(), and seqsubmit_split::CSeqSubSplitter::xWrapSeqEntries().
void CSeq_entry_Base::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 97 of file Seq_entry_.cpp.
References DIAG_COMPILE_INFO, CSeq_entry_Base::m_choice, and CSeq_entry_Base::sm_SelectionNames.
Referenced by CSeq_entry_Base::CheckSelected().
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Which variant is currently selected.
Definition at line 228 of file Seq_entry_.hpp.
References CSeq_entry_Base::m_choice.
Referenced by CTable2AsnContext::ApplyCreateUpdateDates(), CAutogeneratedCleanup::BasicCleanupSeqEntry(), CGapsEditor::ConvertNs2Gaps(), CBlobSplitterImpl::CopySkeleton(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), CFeatureTableReader::FindOpenReadingFrame(), CSeq_entry::GetAnnot(), CSeq_entry::GetDescr(), CSeq_entry::GetLabel(), CSeq_entry::IsSetAnnot(), CSeq_entry::IsSetDescr(), CAsn2FastaApp::ObtainSeqEntryFromSeqEntry(), CAsn2FlatApp::ObtainSeqEntryFromSeqEntry(), CSeq_entry::Parentize(), CSeq_entry::ParentizeOneLevel(), SegMaskerApplication::Run(), CWinMaskApplication::Run(), CSeq_entry::SetAnnot(), CSeq_entry::SetDescr(), CFastaOstream::Write(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E(), CSeq_entry_Info::x_SetObject(), and CFeatureTableReader::xMergeCDSFeatures_impl().
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Definition at line 213 of file Bioseq_set_.cpp.
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Definition at line 166 of file Seq_entry_.cpp.
References CSeq_entry_Base::Reset().
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Definition at line 503 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetAnnot(), CBioseq_set_Base::ResetAnnot(), and CBioseq_set_Base::SetAnnot().
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Definition at line 209 of file Seq_entry_.hpp.
Referenced by CSeq_entry_Base::CheckSelected(), CSeq_entry_Base::DoSelect(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CSeq_entry_Base::Reset(), CSeq_entry_Base::ResetSelection(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), CSeq_entry_Base::ThrowInvalidSelection(), and CSeq_entry_Base::Which().
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Definition at line 498 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetClass(), CBioseq_set_Base::ResetClass(), and CBioseq_set_Base::SetClass().
Definition at line 496 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetColl(), CBioseq_set_Base::IsSetColl(), CBioseq_set_Base::ResetColl(), and CBioseq_set_Base::SetColl().
Definition at line 500 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetDate(), CBioseq_set_Base::IsSetDate(), CBioseq_set_Base::ResetDate(), and CBioseq_set_Base::SetDate().
Definition at line 501 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetDescr(), CBioseq_set_Base::IsSetDescr(), CBioseq_set_Base::ResetDescr(), and CBioseq_set_Base::SetDescr().
Definition at line 495 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetId(), CBioseq_set_Base::IsSetId(), CBioseq_set_Base::ResetId(), and CBioseq_set_Base::SetId().
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Definition at line 497 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetLevel(), CBioseq_set_Base::ResetLevel(), and CBioseq_set_Base::SetLevel().
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Definition at line 215 of file Seq_entry_.hpp.
Referenced by CSeq_entry_Base::DoSelect(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::ResetSelection(), CSeq_entry_Base::SetSeq(), and CSeq_entry_Base::SetSet().
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Definition at line 499 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetRelease(), CBioseq_set_Base::ResetRelease(), and CBioseq_set_Base::SetRelease().
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Definition at line 502 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::GetSeq_set(), CBioseq_set_Base::ResetSeq_set(), and CBioseq_set_Base::SetSeq_set().
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Definition at line 494 of file Bioseq_set_.hpp.
Referenced by CBioseq_set_Base::CBioseq_set_Base(), CBioseq_set_Base::IsSetAnnot(), CBioseq_set_Base::IsSetClass(), CBioseq_set_Base::IsSetLevel(), CBioseq_set_Base::IsSetRelease(), CBioseq_set_Base::IsSetSeq_set(), CBioseq_set_Base::ResetAnnot(), CBioseq_set_Base::ResetClass(), CBioseq_set_Base::ResetLevel(), CBioseq_set_Base::ResetRelease(), CBioseq_set_Base::ResetSeq_set(), CBioseq_set_Base::SetAnnot(), CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetLevel(), CBioseq_set_Base::SetRelease(), and CBioseq_set_Base::SetSeq_set().
Definition at line 213 of file Seq_entry_.hpp.
Referenced by CSeq_entry_Base::SelectionName(), and CSeq_entry_Base::ThrowInvalidSelection().