NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Enumerator | Functions | Variables
Code generated by DATATOOL from 'seqset.asn' (module 'NCBI-Seqset')
+ Collaboration diagram for Code generated by DATATOOL from 'seqset.asn' (module 'NCBI-Seqset'):

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
 

Enumerations

enum  CBioseq_set_Base::EClass {
  CBioseq_set_Base::eClass_not_set = 0 , CBioseq_set_Base::eClass_nuc_prot = 1 , CBioseq_set_Base::eClass_segset = 2 , CBioseq_set_Base::eClass_conset = 3 ,
  CBioseq_set_Base::eClass_parts = 4 , CBioseq_set_Base::eClass_gibb = 5 , CBioseq_set_Base::eClass_gi = 6 , CBioseq_set_Base::eClass_genbank = 7 ,
  CBioseq_set_Base::eClass_pir = 8 , CBioseq_set_Base::eClass_pub_set = 9 , CBioseq_set_Base::eClass_equiv = 10 , CBioseq_set_Base::eClass_swissprot = 11 ,
  CBioseq_set_Base::eClass_pdb_entry = 12 , CBioseq_set_Base::eClass_mut_set = 13 , CBioseq_set_Base::eClass_pop_set = 14 , CBioseq_set_Base::eClass_phy_set = 15 ,
  CBioseq_set_Base::eClass_eco_set = 16 , CBioseq_set_Base::eClass_gen_prod_set = 17 , CBioseq_set_Base::eClass_wgs_set = 18 , CBioseq_set_Base::eClass_named_annot = 19 ,
  CBioseq_set_Base::eClass_named_annot_prod = 20 , CBioseq_set_Base::eClass_read_set = 21 , CBioseq_set_Base::eClass_paired_end_reads = 22 , CBioseq_set_Base::eClass_small_genome_set = 23 ,
  CBioseq_set_Base::eClass_other = 255
}
 
enum class  CBioseq_set_Base::E_memberIndex {
  CBioseq_set_Base::e__allMandatory = 0 , CBioseq_set_Base::e_id , CBioseq_set_Base::e_coll , CBioseq_set_Base::e_level ,
  CBioseq_set_Base::e_class , CBioseq_set_Base::e_release , CBioseq_set_Base::e_date , CBioseq_set_Base::e_descr ,
  CBioseq_set_Base::e_seq_set , CBioseq_set_Base::e_annot
}
 
enum  CSeq_entry_Base::E_Choice { CSeq_entry_Base::e_not_set = 0 , CSeq_entry_Base::e_Seq , CSeq_entry_Base::e_Set }
 Choice variants. More...
 
enum  CSeq_entry_Base::E_ChoiceStopper { CSeq_entry_Base::e_MaxChoice = 3 }
 Maximum+1 value of the choice variant enumerator. More...
 

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 TIdCBioseq_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...
 
TIdCBioseq_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 TCollCBioseq_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...
 
TCollCBioseq_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...
 
TLevelCBioseq_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...
 
TClassCBioseq_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 TReleaseCBioseq_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)
 
TReleaseCBioseq_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 TDateCBioseq_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...
 
TDateCBioseq_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 TDescrCBioseq_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...
 
TDescrCBioseq_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_setCBioseq_set_Base::GetSeq_set (void) const
 Get the Seq_set member data. More...
 
TSeq_setCBioseq_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 TAnnotCBioseq_set_Base::GetAnnot (void) const
 Get the Annot member data. More...
 
TAnnotCBioseq_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_BaseCBioseq_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 TSeqCSeq_entry_Base::GetSeq (void) const
 Get the variant data. More...
 
TSeqCSeq_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 TSetCSeq_entry_Base::GetSet (void) const
 Get the variant data. More...
 
TSetCSeq_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_BaseCSeq_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< TIdCBioseq_set_Base::m_Id
 
CRef< TCollCBioseq_set_Base::m_Coll
 
int CBioseq_set_Base::m_Level
 
EClass CBioseq_set_Base::m_Class
 
string CBioseq_set_Base::m_Release
 
CRef< TDateCBioseq_set_Base::m_Date
 
CRef< TDescrCBioseq_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
 

Detailed Description

Typedef Documentation

◆ TAnnot

Definition at line 137 of file Bioseq_set_.hpp.

◆ TClass

Definition at line 132 of file Bioseq_set_.hpp.

◆ TColl

Definition at line 130 of file Bioseq_set_.hpp.

◆ TDate

Definition at line 134 of file Bioseq_set_.hpp.

◆ TDescr

Definition at line 135 of file Bioseq_set_.hpp.

◆ TId

Definition at line 129 of file Bioseq_set_.hpp.

◆ TLevel

Definition at line 131 of file Bioseq_set_.hpp.

◆ TmemberIndex

Definition at line 152 of file Bioseq_set_.hpp.

◆ Tparent [1/2]

Definition at line 87 of file Bioseq_set_.hpp.

◆ Tparent [2/2]

Definition at line 75 of file Seq_entry_.hpp.

◆ TRelease

Definition at line 133 of file Bioseq_set_.hpp.

◆ TSeq

Definition at line 145 of file Seq_entry_.hpp.

◆ TSeq_set

Definition at line 136 of file Bioseq_set_.hpp.

◆ TSet

Definition at line 146 of file Seq_entry_.hpp.

Enumeration Type Documentation

◆ E_Choice

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Seq 
e_Set 

Definition at line 87 of file Seq_entry_.hpp.

◆ E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Set+1

Definition at line 93 of file Seq_entry_.hpp.

◆ E_memberIndex

Enumerator
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.

◆ EClass

Enumerator
eClass_not_set 
eClass_nuc_prot 

nuc acid and coded proteins

eClass_segset 

segmented sequence + parts

eClass_conset 

constructed sequence + parts

eClass_parts 

parts for 2 or 3

eClass_gibb 

geninfo backbone

eClass_gi 

geninfo

eClass_genbank 

converted genbank

eClass_pir 

converted pir

eClass_pub_set 

all the seqs from a single publication

eClass_equiv 

a set of equivalent maps or seqs

eClass_swissprot 

converted SWISSPROT

eClass_pdb_entry 

a complete PDB entry

eClass_mut_set 

set of mutations

eClass_pop_set 

population study

eClass_phy_set 

phylogenetic study

eClass_eco_set 

ecological sample study

eClass_gen_prod_set 

genomic products, chrom+mRNA+protein

eClass_wgs_set 

whole genome shotgun project

eClass_named_annot 

named annotation set

eClass_named_annot_prod 

with instantiated mRNA+protein

eClass_read_set 

set from a single read

eClass_paired_end_reads 

paired sequences within a read-set

eClass_small_genome_set 

viral segments or mitochondrial minicircles

eClass_other 

Definition at line 97 of file Bioseq_set_.hpp.

Function Documentation

◆ CanGetAnnot()

bool CBioseq_set_Base::CanGetAnnot ( void  ) const
inline

Check if it is safe to call GetAnnot method.

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

Definition at line 775 of file Bioseq_set_.hpp.

Referenced by CAttachedHandles::Attach(), and ReplaceWellknownSeqs().

◆ CanGetClass()

bool CBioseq_set_Base::CanGetClass ( void  ) const
inline

Check if it is safe to call GetClass method.

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

Definition at line 611 of file Bioseq_set_.hpp.

Referenced by CWithdrawSequences::GetNames(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::TakeFromSet(), and CTopLevelSeqEntryContext::x_InitSeqs().

◆ CanGetColl()

bool CBioseq_set_Base::CanGetColl ( void  ) const
inline

Check if it is safe to call GetColl method.

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

Definition at line 543 of file Bioseq_set_.hpp.

References CBioseq_set_Base::IsSetColl().

Referenced by CBioseq_set_Base::GetColl().

◆ CanGetDate()

bool CBioseq_set_Base::CanGetDate ( void  ) const
inline

Check if it is safe to call GetDate method.

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

Definition at line 708 of file Bioseq_set_.hpp.

References CBioseq_set_Base::IsSetDate().

Referenced by CBioseq_set_Base::GetDate().

◆ CanGetDescr()

bool CBioseq_set_Base::CanGetDescr ( void  ) const
inline

Check if it is safe to call GetDescr method.

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

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().

◆ CanGetId()

bool CBioseq_set_Base::CanGetId ( void  ) const
inline

Check if it is safe to call GetId method.

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

Definition at line 522 of file Bioseq_set_.hpp.

References CBioseq_set_Base::IsSetId().

Referenced by CBioseq_set_Base::GetId().

◆ CanGetLevel()

bool CBioseq_set_Base::CanGetLevel ( void  ) const
inline

Check if it is safe to call GetLevel method.

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

Definition at line 564 of file Bioseq_set_.hpp.

References CBioseq_set_Base::IsSetLevel().

Referenced by CBioseq_set_Base::GetLevel().

◆ CanGetRelease()

bool CBioseq_set_Base::CanGetRelease ( void  ) const
inline

Check if it is safe to call GetRelease method.

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

Definition at line 661 of file Bioseq_set_.hpp.

References CBioseq_set_Base::IsSetRelease().

Referenced by CBioseq_set_Base::GetRelease().

◆ CanGetSeq_set()

bool CBioseq_set_Base::CanGetSeq_set ( void  ) const
inline

◆ CBioseq_set_Base() [1/2]

CBioseq_set_Base::CBioseq_set_Base ( const CBioseq_set_Base )
private

◆ CBioseq_set_Base() [2/2]

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.

◆ CheckSelected()

void CSeq_entry_Base::CheckSelected ( E_Choice  index) const
inline

Verify selection, throw exception if it differs from the expected.

Parameters
indexExpected 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().

◆ CSeq_entry_Base() [1/2]

CSeq_entry_Base::CSeq_entry_Base ( const CSeq_entry_Base )
private

◆ CSeq_entry_Base() [2/2]

END_CHOICE_INFO CSeq_entry_Base::CSeq_entry_Base ( void  )

Definition at line 160 of file Seq_entry_.cpp.

◆ DECLARE_INTERNAL_TYPE_INFO() [1/2]

CBioseq_set_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [2/2]

CSeq_entry_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DoSelect()

void CSeq_entry_Base::DoSelect ( E_Choice  index,
CObjectMemoryPool pool = 0 
)
private

◆ EClass()

static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME() CBioseq_set_Base::EClass ( void  )
static

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

◆ GetAnnot()

const CBioseq_set_Base::TAnnot & CBioseq_set_Base::GetAnnot ( void  ) const
inline

◆ GetClass()

CBioseq_set_Base::TClass CBioseq_set_Base::GetClass ( void  ) const
inline

Get the Class member data.

Returns
Copy of the 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(), CValidErrorFormat::GetBioseqSetLabel(), 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(), CValidError_imp::PostErr(), 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().

◆ GetColl()

const CBioseq_set_Base::TColl & CBioseq_set_Base::GetColl ( void  ) const
inline

Get the Coll member data.

Returns
Reference to the 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().

◆ GetDate()

const CBioseq_set_Base::TDate & CBioseq_set_Base::GetDate ( void  ) const
inline

Get the Date member data.

Returns
Reference to the 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().

◆ GetDescr()

const CBioseq_set_Base::TDescr & CBioseq_set_Base::GetDescr ( void  ) const
inline

◆ GetId()

const CBioseq_set_Base::TId & CBioseq_set_Base::GetId ( void  ) const
inline

Get the Id member data.

Returns
Reference to the 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().

◆ GetLevel()

CBioseq_set_Base::TLevel CBioseq_set_Base::GetLevel ( void  ) const
inline

◆ GetRelease()

const CBioseq_set_Base::TRelease & CBioseq_set_Base::GetRelease ( void  ) const
inline

Get the Release member data.

Returns
Reference to the 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().

◆ GetSeq()

const CSeq_entry_Base::TSeq & CSeq_entry_Base::GetSeq ( void  ) const

Get the variant data.

Returns
Reference to the 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(), 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().

◆ GetSeq_set()

const CBioseq_set_Base::TSeq_set & CBioseq_set_Base::GetSeq_set ( void  ) const
inline

Get the Seq_set member data.

Returns
Reference to the 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(), 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_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::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().

◆ GetSet()

const CSeq_entry_Base::TSet & CSeq_entry_Base::GetSet ( void  ) const

Get the variant data.

Returns
Reference to the 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_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_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().

◆ IsSeq()

bool CSeq_entry_Base::IsSeq ( void  ) const
inline

Check if variant Seq is selected.

Seq type is defined as 'typedef CBioseq TSeq'.

Returns
  • true, if the variant is selected.
  • false, otherwise.

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_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(), 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().

◆ IsSet()

bool CSeq_entry_Base::IsSet ( void  ) const
inline

Check if variant Set is selected.

Set type is defined as 'typedef CBioseq_set TSet'.

Returns
  • true, if the variant is selected.
  • false, otherwise.

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_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_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(), 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().

◆ IsSetAnnot()

bool CBioseq_set_Base::IsSetAnnot ( void  ) const
inline

◆ IsSetClass()

bool CBioseq_set_Base::IsSetClass ( void  ) const
inline

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'

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

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(), CValidErrorFormat::GetBioseqSetLabel(), CBioseq_set::GetLabel(), CDeflineProcess::IndexedProcess(), CValidError_imp::IsHugeSet(), MoveAnnotToTop(), MoveBiomolToTop(), CSegregateSetsBase::MoveDescrToEntries(), CBioseq_set::NeedsDocsumTitle(), seqsubmit_split::NeedToProcess(), CConvertSetTypeDlg::OnTreebookSelChanged(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), 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().

◆ IsSetColl()

bool CBioseq_set_Base::IsSetColl ( void  ) const
inline

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'

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

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().

◆ IsSetDate()

bool CBioseq_set_Base::IsSetDate ( void  ) const
inline

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

Data member Date is optional; its type is defined as 'typedef CDate TDate'

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

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().

◆ IsSetDescr()

bool CBioseq_set_Base::IsSetDescr ( void  ) const
inline

◆ IsSetId()

bool CBioseq_set_Base::IsSetId ( void  ) const
inline

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

Data member Id is optional; its type is defined as 'typedef CObject_id TId'

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

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().

◆ IsSetLevel()

bool CBioseq_set_Base::IsSetLevel ( void  ) const
inline

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'

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

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().

◆ IsSetRelease()

bool CBioseq_set_Base::IsSetRelease ( void  ) const
inline

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

Data member Release is optional; its type is defined as 'typedef string TRelease'

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

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().

◆ IsSetSeq_set()

bool CBioseq_set_Base::IsSetSeq_set ( void  ) const
inline

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'

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

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(), 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_GetSeqFromSet(), s_GetSourceDescriptors(), s_HasTopSetSiblings(), s_ScanWhilePossibleNPSet(), s_UpdateFeatureIds(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), CSplitCacheApp::TestSplitBioseq(), CCmdInsertBioseqSet::Unexecute(), 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().

◆ operator=() [1/2]

CBioseq_set_Base& CBioseq_set_Base::operator= ( const CBioseq_set_Base )
private

◆ operator=() [2/2]

CSeq_entry_Base& CSeq_entry_Base::operator= ( const CSeq_entry_Base )
private

◆ Reset() [1/2]

void CBioseq_set_Base::Reset ( void  )
virtual

◆ Reset() [2/2]

void CSeq_entry_Base::Reset ( void  )
virtual

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().

◆ ResetAnnot()

void CBioseq_set_Base::ResetAnnot ( void  )

◆ ResetClass()

void CBioseq_set_Base::ResetClass ( void  )
inline

◆ ResetColl()

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().

◆ ResetDate()

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().

◆ ResetDescr()

void CBioseq_set_Base::ResetDescr ( void  )

◆ ResetId()

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().

◆ ResetLevel()

void CBioseq_set_Base::ResetLevel ( void  )
inline

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().

◆ ResetRelease()

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().

◆ ResetSelection()

void CSeq_entry_Base::ResetSelection ( void  )
virtual

◆ ResetSeq_set()

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().

◆ Select() [1/2]

void CSeq_entry_Base::Select ( E_Choice  index,
EResetVariant  reset,
CObjectMemoryPool pool 
)

Select the requested variant if needed, allocating CObject variants from memory pool.

◆ Select() [2/2]

void CSeq_entry_Base::Select ( E_Choice  index,
EResetVariant  reset = eDoResetVariant 
)

Select the requested variant if needed.

Parameters
indexNew selection state.
resetFlag 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().

◆ SelectionName()

NCBI_NS_STD::string CSeq_entry_Base::SelectionName ( E_Choice  index)
static

Retrieve selection name (for diagnostic purposes).

Parameters
indexOne of possible selection states.
Returns
Name string.

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().

◆ SetAnnot()

CBioseq_set_Base::TAnnot & CBioseq_set_Base::SetAnnot ( void  )
inline

Assign a value to Annot data member.

Returns
Reference to the data value.

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().

◆ SetClass() [1/2]

void CBioseq_set_Base::SetClass ( CBioseq_set_Base::TClass  value)
inline

◆ SetClass() [2/2]

CBioseq_set_Base::TClass & CBioseq_set_Base::SetClass ( void  )
inline

Assign a value to Class data member.

Returns
Reference to the data value.

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().

◆ SetColl() [1/2]

void CBioseq_set_Base::SetColl ( CBioseq_set_Base::TColl value)

Assign a value to Coll data member.

Parameters
valueReference 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().

◆ SetColl() [2/2]

CBioseq_set_Base::TColl & CBioseq_set_Base::SetColl ( void  )

Assign a value to Coll data member.

Returns
Reference to the data value.

Definition at line 115 of file Bioseq_set_.cpp.

References CBioseq_set_Base::m_Coll.

◆ SetDate() [1/2]

void CBioseq_set_Base::SetDate ( CBioseq_set_Base::TDate value)

Assign a value to Date data member.

Parameters
valueReference 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().

◆ SetDate() [2/2]

CBioseq_set_Base::TDate & CBioseq_set_Base::SetDate ( void  )

Assign a value to Date data member.

Returns
Reference to the data value.

Definition at line 138 of file Bioseq_set_.cpp.

References CBioseq_set_Base::m_Date.

◆ SetDefaultClass()

void CBioseq_set_Base::SetDefaultClass ( void  )
inline

Assign default value to Class data member.

Definition at line 624 of file Bioseq_set_.hpp.

References CBioseq_set_Base::ResetClass().

◆ SetDescr() [1/2]

void CBioseq_set_Base::SetDescr ( CBioseq_set_Base::TDescr value)

◆ SetDescr() [2/2]

CBioseq_set_Base::TDescr & CBioseq_set_Base::SetDescr ( void  )

Assign a value to Descr data member.

Returns
Reference to the data value.

Definition at line 155 of file Bioseq_set_.cpp.

References CBioseq_set_Base::m_Descr.

◆ SetId() [1/2]

void CBioseq_set_Base::SetId ( CBioseq_set_Base::TId value)

◆ SetId() [2/2]

CBioseq_set_Base::TId & CBioseq_set_Base::SetId ( void  )

Assign a value to Id data member.

Returns
Reference to the data value.

Definition at line 98 of file Bioseq_set_.cpp.

References CBioseq_set_Base::m_Id.

◆ SetLevel() [1/2]

void CBioseq_set_Base::SetLevel ( CBioseq_set_Base::TLevel  value)
inline

◆ SetLevel() [2/2]

CBioseq_set_Base::TLevel & CBioseq_set_Base::SetLevel ( void  )
inline

Assign a value to Level data member.

Returns
Reference to the data value.

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().

◆ SetRelease() [1/3]

void CBioseq_set_Base::SetRelease ( const TRelease value)
inline

Assign a value to Release data member.

Parameters
valueValue 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().

◆ SetRelease() [2/3]

void CBioseq_set_Base::SetRelease ( CBioseq_set_Base::TRelease &&  value)
inline

◆ SetRelease() [3/3]

CBioseq_set_Base::TRelease & CBioseq_set_Base::SetRelease ( void  )
inline

Assign a value to Release data member.

Returns
Reference to the data value.

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().

◆ SetSeq() [1/2]

void CSeq_entry_Base::SetSeq ( CSeq_entry_Base::TSeq value)

Select the variant and set its data.

Parameters
valueReference 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.

◆ SetSeq() [2/2]

CSeq_entry_Base::TSeq & CSeq_entry_Base::SetSeq ( void  )

Select the variant.

Returns
Reference to the variant data.

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().

◆ SetSeq_set()

CBioseq_set_Base::TSeq_set & CBioseq_set_Base::SetSeq_set ( void  )
inline

Assign a value to Seq_set data member.

Returns
Reference to the data value.

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().

◆ SetSet() [1/2]

void CSeq_entry_Base::SetSet ( CSeq_entry_Base::TSet value)

Select the variant and set its data.

Parameters
valueReference 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.

◆ SetSet() [2/2]

CSeq_entry_Base::TSet & CSeq_entry_Base::SetSet ( void  )

Select the variant.

Returns
Reference to the variant data.

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(), CReadEntryHook::ReadObject(), 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().

◆ ThrowInvalidSelection()

void CSeq_entry_Base::ThrowInvalidSelection ( E_Choice  index) const

Throw 'InvalidSelection' exception.

Parameters
indexExpected 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().

◆ Which()

CSeq_entry_Base::E_Choice CSeq_entry_Base::Which ( void  ) const
inline

◆ ~CBioseq_set_Base()

CBioseq_set_Base::~CBioseq_set_Base ( void  )
virtual

Definition at line 213 of file Bioseq_set_.cpp.

◆ ~CSeq_entry_Base()

CSeq_entry_Base::~CSeq_entry_Base ( void  )
virtual

Definition at line 166 of file Seq_entry_.cpp.

References CSeq_entry_Base::Reset().

Variable Documentation

◆ m_Annot

list< CRef< CSeq_annot > > CBioseq_set_Base::m_Annot
private

◆ m_choice

E_Choice CSeq_entry_Base::m_choice
private

◆ m_Class

EClass CBioseq_set_Base::m_Class
private

◆ m_Coll

CRef< TColl > CBioseq_set_Base::m_Coll
private

◆ m_Date

CRef< TDate > CBioseq_set_Base::m_Date
private

◆ m_Descr

CRef< TDescr > CBioseq_set_Base::m_Descr
private

◆ m_Id

CRef< TId > CBioseq_set_Base::m_Id
private

◆ m_Level

int CBioseq_set_Base::m_Level
private

◆ m_object

NCBI_NS_NCBI::CSerialObject* CSeq_entry_Base::m_object
private

◆ m_Release

string CBioseq_set_Base::m_Release
private

◆ m_Seq_set

list< CRef< CSeq_entry > > CBioseq_set_Base::m_Seq_set
private

◆ m_set_State

Uint4 CBioseq_set_Base::m_set_State[1]
private

◆ sm_SelectionNames

const char *const CSeq_entry_Base::sm_SelectionNames
staticprivate
Initial value:
= {
"not set",
"seq",
"set"
}

Definition at line 213 of file Seq_entry_.hpp.

Referenced by CSeq_entry_Base::SelectionName(), and CSeq_entry_Base::ThrowInvalidSelection().

Modified on Thu May 30 12:21:14 2024 by modify_doxy.py rev. 669887