CBioseq_Handle Class Reference
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#include <bioseq_handle.hpp>

Inheritance diagram for CBioseq_Handle:

[legend]Collaboration diagram for CBioseq_Handle:

[legend]List of all members.

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Detailed Description

CBioseq_Handle --.

Proxy to access the bioseq data

Definition at line 90 of file bioseq_handle.hpp.

Public Types
typedef int	TBioseqStateFlags
typedef CConstRef< CBioseq >	TBioseqCore
	Bioseq core -- using partially populated CBioseq.
typedef CBioseq	TObject
	Unified interface for templates.
typedef vector< CSeq_id_Handle >	TId
typedef CSeq_descr	TDescr
typedef CSeq_inst	TInst
typedef TInst::TRepr	TInst_Repr
typedef TInst::TMol	TInst_Mol
typedef TInst::TLength	TInst_Length
typedef TInst::TFuzz	TInst_Fuzz
typedef TInst::TTopology	TInst_Topology
typedef TInst::TStrand	TInst_Strand
typedef TInst::TSeq_data	TInst_Seq_data
typedef TInst::TExt	TInst_Ext
typedef TInst::THist	TInst_Hist
typedef CSeq_inst::TMol	TMol
enum	EBioseqStateFlags {   fState_none = 0, fState_suppress_temp = 1 << 0, fState_suppress_perm = 1 << 1, fState_suppress,   fState_dead = 1 << 2, fState_confidential = 1 << 3, fState_withdrawn = 1 << 4, fState_no_data = 1 << 5,   fState_conflict = 1 << 6, fState_not_found = 1 << 7, fState_other_error = 1 << 8 }
	State of bioseq handle. More...
enum	EFindSegment { eFindSegment_NoLimit, eFindSegment_LimitTSE }
	Segment search flags. More...
enum	EVectorCoding { eCoding_NotSet, eCoding_Ncbi, eCoding_Iupac }
	CSeqVector constructor flags. More...
enum	EVectorStrand { eStrand_Plus, eStrand_Minus }
enum	EFeatureFetchPolicy { eFeatureFetchPolicy_default = 0, eFeatureFetchPolicy_only_near = 1 }
	Feature fetch policy describes when to look for features on sequence segments. More...
Public Member Functions
	CBioseq_Handle (void)
void	Reset (void)
	Reset handle and make it not to point to any bioseq.
CScope &	GetScope (void) const
	Get scope this handle belongs to.
CConstRef< CSeq_id >	GetSeqId (void) const
	Get id which can be used to access this bioseq handle Throws an exception if none is available.
CConstRef< CSeq_id >	GetInitialSeqIdOrNull (void) const
	Get id used to obtain this bioseq handle.
const CBioObjectId &	GetBioObjectId (void) const
	Get unique object id.
const CSeq_id_Handle &	GetSeq_id_Handle (void) const
	Get handle of id used to obtain this bioseq handle.
CSeq_id_Handle	GetAccessSeq_id_Handle (void) const
	Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's non-null.
TBioseqStateFlags	GetState (void) const
	Get state of the bioseq.
bool	State_SuppressedTemp (void) const
bool	State_SuppressedPerm (void) const
bool	State_Suppressed (void) const
bool	State_Confidential (void) const
bool	State_Dead (void) const
bool	State_Withdrawn (void) const
bool	State_NoData (void) const
bool	State_Conflict (void) const
bool	State_NotFound (void) const
bool	IsSynonym (const CSeq_id &id) const
	Check if this id can be used to obtain this bioseq handle.
bool	IsSynonym (const CSeq_id_Handle &idh) const
CConstRef< CSynonymsSet >	GetSynonyms (void) const
	Get the bioseq's synonyms.
CSeq_entry_Handle	GetParentEntry (void) const
	Get parent Seq-entry handle.
CBioseq_set_Handle	GetParentBioseq_set (void) const
	Return a handle for the parent Bioseq-set, or null handle.
CSeq_entry_Handle	GetSeq_entry_Handle (void) const
	Get parent Seq-entry handle.
CSeq_entry_Handle	GetTopLevelEntry (void) const
	Get top level Seq-entry handle.
CBioseq_EditHandle	GetEditHandle (void) const
	Get 'edit' version of handle.
TBioseqCore	GetBioseqCore (void) const
	Get bioseq core structure.
CConstRef< CBioseq >	GetCompleteBioseq (void) const
	Get the complete bioseq.
CConstRef< TObject >	GetCompleteObject (void) const
CConstRef< TObject >	GetObjectCore (void) const
bool	IsSetId (void) const
bool	CanGetId (void) const
const TId &	GetId (void) const
bool	IsSetDescr (void) const
bool	CanGetDescr (void) const
const TDescr &	GetDescr (void) const
bool	IsSetInst (void) const
bool	CanGetInst (void) const
const TInst &	GetInst (void) const
bool	IsSetInst_Repr (void) const
bool	CanGetInst_Repr (void) const
TInst_Repr	GetInst_Repr (void) const
bool	IsSetInst_Mol (void) const
bool	CanGetInst_Mol (void) const
TInst_Mol	GetInst_Mol (void) const
bool	IsSetInst_Length (void) const
bool	CanGetInst_Length (void) const
TInst_Length	GetInst_Length (void) const
TSeqPos	GetBioseqLength (void) const
bool	IsSetInst_Fuzz (void) const
bool	CanGetInst_Fuzz (void) const
const TInst_Fuzz &	GetInst_Fuzz (void) const
bool	IsSetInst_Topology (void) const
bool	CanGetInst_Topology (void) const
TInst_Topology	GetInst_Topology (void) const
bool	IsSetInst_Strand (void) const
bool	CanGetInst_Strand (void) const
TInst_Strand	GetInst_Strand (void) const
bool	IsSetInst_Seq_data (void) const
bool	CanGetInst_Seq_data (void) const
const TInst_Seq_data &	GetInst_Seq_data (void) const
bool	IsSetInst_Ext (void) const
bool	CanGetInst_Ext (void) const
const TInst_Ext &	GetInst_Ext (void) const
bool	IsSetInst_Hist (void) const
bool	CanGetInst_Hist (void) const
const TInst_Hist &	GetInst_Hist (void) const
bool	HasAnnots (void) const
TMol	GetSequenceType (void) const
bool	IsProtein (void) const
bool	IsNucleotide (void) const
CSeq_entry_Handle	GetComplexityLevel (CBioseq_set::EClass cls) const
	Go up to a certain complexity level (or the nearest level of the same priority if the required class is not found): level class 0 not-set (0) , 3 nuc-prot (1) , -- nuc acid and coded proteins 2 segset (2) , -- segmented sequence + parts 2 conset (3) , -- constructed sequence + parts 1 parts (4) , -- parts for 2 or 3 1 gibb (5) , -- geninfo backbone 1 gi (6) , -- geninfo 5 genbank (7) , -- converted genbank 3 pir (8) , -- converted pir 4 pub-set (9) , -- all the seqs from a single publication 4 equiv (10) , -- a set of equivalent maps or seqs 3 swissprot (11) , -- converted SWISSPROT 3 pdb-entry (12) , -- a complete PDB entry 4 mut-set (13) , -- set of mutations 4 pop-set (14) , -- population study 4 phy-set (15) , -- phylogenetic study 4 eco-set (16) , -- ecological sample study 4 gen-prod-set (17) , -- genomic products, chrom+mRNa+protein 4 wgs-set (18) , -- whole genome shotgun project 0 other (255).
CSeq_entry_Handle	GetExactComplexityLevel (CBioseq_set::EClass cls) const
	Return level with exact complexity, or empty handle if not found.
TMol	GetBioseqMolType (void) const
	Get some values from core:.
bool	IsNa (void) const
bool	IsAa (void) const
const CSeqMap &	GetSeqMap (void) const
	Get sequence map.
bool	ContainsSegment (const CSeq_id &id, size_t resolve_depth=kMax_Int, EFindSegment limit_flag=eFindSegment_NoLimit) const
	Check if the seq-id describes a segment of the bioseq.
bool	ContainsSegment (CSeq_id_Handle id, size_t resolve_depth=kMax_Int, EFindSegment limit_flag=eFindSegment_NoLimit) const
bool	ContainsSegment (const CBioseq_Handle &part, size_t resolve_depth=kMax_Int, EFindSegment limit_flag=eFindSegment_NoLimit) const
CSeqVector	GetSeqVector (EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const
	Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.
CSeqVector	GetSeqVector (ENa_strand strand=eNa_strand_plus) const
	Get sequence.
CSeqVector	GetSeqVector (EVectorCoding coding, EVectorStrand strand) const
	Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.
CSeqVector	GetSeqVector (EVectorStrand strand) const
	Get sequence.
CRef< CSeq_loc >	GetRangeSeq_loc (TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const
	Return CSeq_loc referencing the given range and strand on the bioseq If start == 0, stop == 0, and strand == eNa_strand_unknown, CSeq_loc will be of type 'whole'.
CRef< CSeq_loc >	MapLocation (const CSeq_loc &loc) const
	Map a seq-loc from the bioseq's segment to the bioseq.
bool	operator== (const CBioseq_Handle &h) const
	Check if handles point to the same bioseq.
bool	operator!= (const CBioseq_Handle &h) const
bool	operator< (const CBioseq_Handle &h) const
	For usage in containers.
	DECLARE_OPERATOR_BOOL (m_Info.IsValid())
	Check if handle points to a bioseq and is not removed.
bool	IsRemoved (void) const
	Check if handle points to a removed bioseq.
const CTSE_Handle &	GetTSE_Handle (void) const
	Get CTSE_Handle of containing TSE.
CBioseq_EditHandle	CopyTo (const CSeq_entry_EditHandle &entry, int index=-1) const
CBioseq_EditHandle	CopyTo (const CBioseq_set_EditHandle &seqset, int index=-1) const
	Copy current bioseq into seqset.
CBioseq_EditHandle	CopyToSeq (const CSeq_entry_EditHandle &entry) const
	Copy current bioseq into seq-entry and set seq-entry as bioseq.
bool	AddUsedBioseq (const CBioseq_Handle &bh) const
	Register argument bioseq as used by this bioseq, so it will be released by scope only after this bioseq is released.
EFeatureFetchPolicy	GetFeatureFetchPolicy (void) const
const CBioseq_Info &	x_GetInfo (void) const
Protected Types
typedef CBioseq_ScopeInfo	TScopeInfo
typedef CScopeInfo_Ref< TScopeInfo >	TLock
Protected Member Functions
	CBioseq_Handle (const CSeq_id_Handle &id, const TScopeInfo &info)
	CBioseq_Handle (const CSeq_id_Handle &id, const TLock &lock)
CScope_Impl &	x_GetScopeImpl (void) const
const CBioseq_ScopeInfo &	x_GetScopeInfo (void) const
Protected Attributes
CSeq_id_Handle	m_Handle_Seq_id
TLock	m_Info
Friends
class	CScope_Impl
class	CSynonymsSet
class	CSeq_entry_EditHandle

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Member Typedef Documentation

typedef CConstRef<CBioseq> CBioseq_Handle::TBioseqCore

Bioseq core -- using partially populated CBioseq. Definition at line 178 of file bioseq_handle.hpp.

typedef int CBioseq_Handle::TBioseqStateFlags

Definition at line 134 of file bioseq_handle.hpp.

typedef CSeq_descr CBioseq_Handle::TDescr

Definition at line 199 of file bioseq_handle.hpp.

typedef vector<CSeq_id_Handle> CBioseq_Handle::TId

Definition at line 194 of file bioseq_handle.hpp.

typedef CSeq_inst CBioseq_Handle::TInst

Definition at line 204 of file bioseq_handle.hpp.

typedef TInst::TExt CBioseq_Handle::TInst_Ext

Definition at line 245 of file bioseq_handle.hpp.

typedef TInst::TFuzz CBioseq_Handle::TInst_Fuzz

Definition at line 225 of file bioseq_handle.hpp.

typedef TInst::THist CBioseq_Handle::TInst_Hist

Definition at line 250 of file bioseq_handle.hpp.

typedef TInst::TLength CBioseq_Handle::TInst_Length

Definition at line 219 of file bioseq_handle.hpp.

typedef TInst::TMol CBioseq_Handle::TInst_Mol

Definition at line 214 of file bioseq_handle.hpp.

typedef TInst::TRepr CBioseq_Handle::TInst_Repr

Definition at line 209 of file bioseq_handle.hpp.

typedef TInst::TSeq_data CBioseq_Handle::TInst_Seq_data

Definition at line 240 of file bioseq_handle.hpp.

typedef TInst::TStrand CBioseq_Handle::TInst_Strand

Definition at line 235 of file bioseq_handle.hpp.

typedef TInst::TTopology CBioseq_Handle::TInst_Topology

Definition at line 230 of file bioseq_handle.hpp.

typedef CScopeInfo_Ref<TScopeInfo> CBioseq_Handle::TLock [protected]

Definition at line 457 of file bioseq_handle.hpp.

typedef CSeq_inst::TMol CBioseq_Handle::TMol

Definition at line 258 of file bioseq_handle.hpp.

typedef CBioseq CBioseq_Handle::TObject

Unified interface for templates. Definition at line 187 of file bioseq_handle.hpp.

typedef CBioseq_ScopeInfo CBioseq_Handle::TScopeInfo [protected]

Definition at line 456 of file bioseq_handle.hpp.

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Member Enumeration Documentation

enum CBioseq_Handle::EBioseqStateFlags

State of bioseq handle. Enumerator: fState_none  fState_suppress_temp  fState_suppress_perm  fState_suppress  fState_dead  fState_confidential  fState_withdrawn  fState_no_data  fState_conflict  fState_not_found  fState_other_error  Definition at line 120 of file bioseq_handle.hpp.

enum CBioseq_Handle::EFeatureFetchPolicy

Feature fetch policy describes when to look for features on sequence segments. Enumerator: eFeatureFetchPolicy_default  eFeatureFetchPolicy_only_near  Definition at line 445 of file bioseq_handle.hpp.

enum CBioseq_Handle::EFindSegment

Segment search flags. Enumerator: eFindSegment_NoLimit  No limit on resolving seq-map. eFindSegment_LimitTSE  Resolve in the parent TSE only. Definition at line 303 of file bioseq_handle.hpp.

enum CBioseq_Handle::EVectorCoding

CSeqVector constructor flags. Enumerator: eCoding_NotSet  Use original coding - DANGEROUS! - may change. eCoding_Ncbi  Set coding to binary coding (Ncbi4na or Ncbistdaa). eCoding_Iupac  Set coding to printable coding (Iupacna or Iupacaa). Definition at line 332 of file bioseq_handle.hpp.

enum CBioseq_Handle::EVectorStrand

Enumerator: eStrand_Plus  Plus strand. eStrand_Minus  Minus strand. Definition at line 337 of file bioseq_handle.hpp.

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Constructor & Destructor Documentation

CBioseq_Handle::CBioseq_Handle (  const CSeq_id_Handle &  id, const TScopeInfo &  info )  [protected]

Definition at line 72 of file bioseq_handle.cpp.

CBioseq_Handle::CBioseq_Handle (  const CSeq_id_Handle &  id, const TLock &  lock )  [protected]

Definition at line 80 of file bioseq_handle.cpp.

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Member Function Documentation

bool CBioseq_Handle::AddUsedBioseq (  const CBioseq_Handle &  bh  )  const

Register argument bioseq as used by this bioseq, so it will be released by scope only after this bioseq is released. Parameters: bh  Used bioseq handle Returns: True if argument bioseq was successfully registered as 'used'. False if argument bioseq was not registered as 'used'. Possible reasons: Circular reference in 'used' tree. Definition at line 1003 of file bioseq_handle.cpp. References CTSE_Handle::AddUsedTSE(), and GetTSE_Handle().

bool CBioseq_Handle::CanGetDescr (  void   )  const

Definition at line 180 of file bioseq_handle.cpp. References CBioseq_Base_Info::CanGetDescr(), and x_GetInfo(). Referenced by CCleanup_imp::x_MergeDuplicatePubs().

bool CBioseq_Handle::CanGetId (  void   )  const

Definition at line 162 of file bioseq_handle.cpp. References CBioseq_Info::CanGetId(), and x_GetInfo(). Referenced by CCleanup_imp::x_ExtendSingleGeneOnmRNA().

bool CBioseq_Handle::CanGetInst (  void   )  const

Definition at line 198 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst(), and x_GetInfo(). Referenced by CAutoDef::GetOneDefLine().

bool CBioseq_Handle::CanGetInst_Ext (  void   )  const

Definition at line 354 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Ext(), and x_GetInfo(). Referenced by s_AddPartToSegmentedBioseq().

bool CBioseq_Handle::CanGetInst_Fuzz (  void   )  const

Definition at line 281 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Fuzz(), and x_GetInfo().

bool CBioseq_Handle::CanGetInst_Hist (  void   )  const

Definition at line 372 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Hist(), and x_GetInfo().

bool CBioseq_Handle::CanGetInst_Length (  void   )  const

Definition at line 252 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Length(), and x_GetInfo().

bool CBioseq_Handle::CanGetInst_Mol (  void   )  const

Definition at line 234 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Mol(), and x_GetInfo(). Referenced by CSeqTextDataSource::IsmRNASequence(), and CSGSegmentsSeqIDJob::x_Execute().

bool CBioseq_Handle::CanGetInst_Repr (  void   )  const

Definition at line 216 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Repr(), and x_GetInfo(). Referenced by CCleanup_imp::x_ChangeCitSub().

bool CBioseq_Handle::CanGetInst_Seq_data (  void   )  const

Definition at line 335 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Seq_data(), and x_GetInfo().

bool CBioseq_Handle::CanGetInst_Strand (  void   )  const

Definition at line 317 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Strand(), and x_GetInfo().

bool CBioseq_Handle::CanGetInst_Topology (  void   )  const

Definition at line 299 of file bioseq_handle.cpp. References CBioseq_Info::CanGetInst_Topology(), and x_GetInfo().

bool CBioseq_Handle::ContainsSegment (  const CBioseq_Handle &  part, size_t  resolve_depth = kMax_Int, EFindSegment  limit_flag = eFindSegment_NoLimit )  const

Definition at line 428 of file bioseq_handle.cpp. References CSeqMap::BeginResolved(), eFindSegment_LimitTSE, CSeqMap::fFindRef, CSeqMap_CI::GetRefSeqid(), GetScope(), GetSeqMap(), GetSynonyms(), GetTopLevelEntry(), SSeqMapSelector::SetFlags(), SSeqMapSelector::SetLimitTSE(), and SSeqMapSelector::SetResolveCount().

bool CBioseq_Handle::ContainsSegment (  CSeq_id_Handle  id, size_t  resolve_depth = kMax_Int, EFindSegment  limit_flag = eFindSegment_NoLimit )  const

Definition at line 452 of file bioseq_handle.cpp. References CSeqMap::BeginResolved(), eFindSegment_LimitTSE, CSeqMap::fFindRef, CScope::GetBioseqHandle(), CSeqMap_CI::GetRefSeqid(), GetScope(), GetSeqMap(), GetSynonyms(), GetTopLevelEntry(), SSeqMapSelector::SetFlags(), SSeqMapSelector::SetLimitTSE(), and SSeqMapSelector::SetResolveCount().

bool CBioseq_Handle::ContainsSegment (  const CSeq_id &  id, size_t  resolve_depth = kMax_Int, EFindSegment  limit_flag = eFindSegment_NoLimit )  const

Check if the seq-id describes a segment of the bioseq. Parameters: id  Seq-id to be checked for being a segment of the handle. resolve_depth  Depth of resolving segments. Zero allows to check only top-level segments. limit_flag  Allow/prohibit resolving far references. By default all segments are resolved. If the flag is set to eFindSegment_LimitTSE, only near references are checked. Definition at line 418 of file bioseq_handle.cpp. References CSeq_id_Handle::GetHandle().

CBioseq_EditHandle CBioseq_Handle::CopyTo (  const CBioseq_set_EditHandle &  seqset, int  index = -1 )  const

Copy current bioseq into seqset. Parameters: entry  Current bioseq will be inserted into seqset pointed by this handle. index  Start index is 0 and -1 means end Returns: Edit handle to inserted bioseq Definition at line 633 of file bioseq_handle.cpp. References CBioseq_set_EditHandle::CopyBioseq().

CBioseq_EditHandle CBioseq_Handle::CopyTo (  const CSeq_entry_EditHandle &  entry, int  index = -1 )  const

Parameters: index  Start index is 0 and -1 means end Returns: Edit handle to inserted bioseq Definition at line 625 of file bioseq_handle.cpp. References CSeq_entry_EditHandle::CopyBioseq().

CBioseq_EditHandle CBioseq_Handle::CopyToSeq (  const CSeq_entry_EditHandle &  entry  )  const

Copy current bioseq into seq-entry and set seq-entry as bioseq. Parameters: entry  Seq-entry pointed by entry handle will be set to bioseq Returns: Edit handle to inserted bioseq Definition at line 641 of file bioseq_handle.cpp. References CSeq_entry_EditHandle::CopySeq().

CBioseq_Handle::DECLARE_OPERATOR_BOOL (  m_Info.  IsValid()  )

Check if handle points to a bioseq and is not removed. See also: operator !()

CSeq_id_Handle CBioseq_Handle::GetAccessSeq_id_Handle (  void   )  const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's non-null. Definition at line 927 of file bioseq_handle.cpp. References _ASSERT, CScope::GetBioseqHandleFromTSE(), GetId(), GetScope(), GetSeq_id_Handle(), GetTSE_Handle(), id, and ITERATE. Referenced by GetRangeSeq_loc(), GetSeqId(), and CAnnot_Collector::x_Initialize().

const CBioObjectId & CBioseq_Handle::GetBioObjectId (  void   )  const

Get unique object id. Definition at line 130 of file bioseq_handle.cpp. References CTSE_Info_Object::GetBioObjectId(), and x_GetInfo(). Referenced by CEditsSaver::Detach().

CBioseq_Handle::TBioseqCore CBioseq_Handle::GetBioseqCore (  void   )  const

Get bioseq core structure. Definition at line 141 of file bioseq_handle.cpp. References CBioseq_Info::GetBioseqCore(), and x_GetInfo(). Referenced by BlastXML_FormatReport(), BOOST_AUTO_TEST_CASE(), CAlnVec::CalculateScore(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), ChangeSeqId(), CValidError_bioseq::CheckSoureDescriptor(), Convert_Seq_id_Bioseq(), CBioseqContext::GetBioseqIds(), GetObjectCore(), CTaxTreeDS_ObjMgr::GetTaxMap(), s_BlastXMLAddIteration(), s_IsLocGEDL(), s_IsLocRefSeqMrna(), s_LocIdType(), s_LocIsNmAccession(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(), CId1FetchApp::WriteQualityScores(), CFastaOstream::WriteTitle(), CSequenceItem::x_GatherInfo(), CDeflineItem::x_GatherInfo(), CAlnGraphic::x_GetAlnInfo(), CAutoDef::x_GetFeatureClauses(), CSequenceDataTester::x_Init(), CShowBlastDefline::x_InitDefline(), and CBlastFormat::x_PrintTabularReport().

TSeqPos CBioseq_Handle::GetBioseqLength (  void   )  const

Definition at line 264 of file bioseq_handle.cpp. References GetInst_Length(), CSeqMap::GetLength(), GetScope(), GetSeqMap(), and IsSetInst_Length(). Referenced by AgpWrite(), CCleanup_imp::BasicCleanup(), BOOST_AUTO_TEST_CASE(), CVisibleRangeEvent::Clamp(), CSeq_loc_Conversion::Convert(), CSeqVector::CSeqVector(), CDefaultLengthGetter::GetLength(), GetLength(), CAutoDef::GetMasterLocation(), GetRangeSeq_loc(), CFeatGlyph::GetTooltip(), s_GetAlignmentTooltip(), s_GetFrame(), s_GetItems_Feat(), s_GetTails(), s_LocIntervalsSpanOrigin(), s_PercentBioseqMatch(), s_SeqAlignSetToXMLHsps(), CCrossAlnRenderer::Update(), CBlastHitMatrix::x_InitPort(), CSeqMap::x_ResolveSegmentLength(), and CHitMatrixWidget::x_SetPortLimits().

CSeq_inst::TMol CBioseq_Handle::GetBioseqMolType (  void   )  const

Get some values from core:. Definition at line 394 of file bioseq_handle.cpp. References GetSequenceType(). Referenced by GetProteinWeights().

CConstRef< CBioseq > CBioseq_Handle::GetCompleteBioseq (  void   )  const

Get the complete bioseq. Definition at line 135 of file bioseq_handle.cpp. References CBioseq_Info::GetCompleteBioseq(), and x_GetInfo(). Referenced by CValidError_imp::AddBioseqWithNoPub(), CValidError_imp::AddProtWithoutFullRef(), CWriteDB_Impl::AddSequence(), CProjectFileWriter::AddToScope(), CEditsSaver::Attach(), BOOST_AUTO_TEST_CASE(), Convert_Seq_id_Bioseq(), CGFFFormatter::FormatSequence(), GetCompleteObject(), GetNucleotideParent(), CwxDemoFeatureTableFrame::LoadAccession(), CwxDemoAlignTableFrame::LoadAccession(), CSelectFeatureDlg::OnButtonSaveFile(), CResolveRequest::Process(), RemoteFetchLongNucleotideBioseq(), RestoreModelFromInternalGnomonFeature(), RestoreModelFromPublicMrnaFeature(), RetrieveGi555WithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), s_ImportQueries(), s_IsNcOrNt(), s_MakeBioseqs(), s_MakeNewMasterSeq(), CFastaOstream::SkipBioseq(), CValidError_imp::ValidateBioSourceForSeq(), CBuildDatabase::x_AddOneRemoteSequence(), CValidError_bioseq::x_DupFeatSeverity(), CValidError_bioseq::x_ValidateCDSmRNAmatch(), and CValidError_bioseq::x_ValidatePubFeatures().

CSeq_entry_Handle CBioseq_Handle::GetComplexityLevel (  CBioseq_set::EClass  cls  )  const

Go up to a certain complexity level (or the nearest level of the same priority if the required class is not found): level class 0 not-set (0) , 3 nuc-prot (1) , -- nuc acid and coded proteins 2 segset (2) , -- segmented sequence + parts 2 conset (3) , -- constructed sequence + parts 1 parts (4) , -- parts for 2 or 3 1 gibb (5) , -- geninfo backbone 1 gi (6) , -- geninfo 5 genbank (7) , -- converted genbank 3 pir (8) , -- converted pir 4 pub-set (9) , -- all the seqs from a single publication 4 equiv (10) , -- a set of equivalent maps or seqs 3 swissprot (11) , -- converted SWISSPROT 3 pdb-entry (12) , -- a complete PDB entry 4 mut-set (13) , -- set of mutations 4 pop-set (14) , -- population study 4 phy-set (15) , -- phylogenetic study 4 eco-set (16) , -- ecological sample study 4 gen-prod-set (17) , -- genomic products, chrom+mRNa+protein 4 wgs-set (18) , -- whole genome shotgun project 0 other (255). Definition at line 575 of file bioseq_handle.cpp. References _ASSERT, CBioseq_set_Base::eClass_other, CSeq_entry_Handle::GetParentEntry(), GetParentEntry(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSeq(), CSeq_entry_Handle::IsSet(), and CBioseq_set_Handle::sx_GetComplexityTable(). Referenced by GetExactComplexityLevel().

const CSeq_descr & CBioseq_Handle::GetDescr (  void   )  const

Definition at line 186 of file bioseq_handle.cpp. References CBioseq_Base_Info::GetDescr(), and x_GetInfo().

CBioseq_EditHandle CBioseq_Handle::GetEditHandle (  void   )  const

Get 'edit' version of handle. Definition at line 147 of file bioseq_handle.cpp. References CScope_Impl::GetEditHandle(), and x_GetScopeImpl(). Referenced by AddBioseqToBioseq(), AddBioseqToBioseqSet(), CAddFeatChecker::Do(), CRemoveFeatChecker::Do(), CRemoveBioseqChecker::Do(), CResetIdChecker::Do(), CRemoveIdChecker::Do(), CAddIdChecker::Do(), CPromote::PromoteCdregion(), CPromote::PromotePub(), CPromote::PromoteRna(), CCleanup_imp::RemoveEmptyFeaturesDescriptorsAndAnnots(), CSeq_entry_EditHandle::SetSeq(), CCleanup_imp::x_ConvertOrgDescToSourceDescriptor(), CCleanup_imp::x_ExtendedCleanupBioSourceDescriptorsAndFeatures(), CCleanup_imp::x_ExtendedCleanupBioSourceFeatures(), CCleanup_imp::x_MergeAdjacentAnnots(), CCleanup_imp::x_MergeDuplicatePubs(), CCleanup_imp::x_MoveDescriptor(), CCleanup_imp::x_RecurseForDescriptors(), CCleanup_imp::x_RecurseForSeqAnnots(), CCleanup_imp::x_RemoveDescrByType(), CCleanup_imp::x_RemoveEmptyFeatureAnnots(), and CBioseqContext::~CBioseqContext().

CSeq_entry_Handle CBioseq_Handle::GetExactComplexityLevel (  CBioseq_set::EClass  cls  )  const

Return level with exact complexity, or empty handle if not found. Definition at line 605 of file bioseq_handle.cpp. References GetComplexityLevel(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSet(), and CSeq_entry_Handle::Reset(). Referenced by CValidError_bioseq::CdError(), GetParentForPart(), s_GetParent(), s_HasSegments(), CBioseqContext::x_HasParts(), CBioseqContext::x_IsInGPS(), CBioseqContext::x_IsInNucProt(), and CPromote::x_PromoteRna().

CBioseq_Handle::EFeatureFetchPolicy CBioseq_Handle::GetFeatureFetchPolicy (  void   )  const

Definition at line 1163 of file bioseq_handle.cpp. References x_GetInfo(). Referenced by CAnnot_Collector::x_Initialize().

const CBioseq_Handle::TId & CBioseq_Handle::GetId (  void   )  const

Definition at line 168 of file bioseq_handle.cpp. References CBioseq_Info::GetId(), and x_GetInfo(). Referenced by CEditsSaver::Attach(), CEditsSaver::Detach(), CResetIds_EditCommand::Do(), GetAccessSeq_id_Handle(), GetId(), GetTitle(), s_GetNameForBioseq(), s_IsRefSeq(), s_PrintIds(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualsProductId(), CCleanup_imp::x_FixPIDDbtag(), CDBSourceItem::x_GatherInfo(), CProjectFileWriter::x_GetGi(), CAnnot_Collector::x_SearchLoc(), CAnnot_Collector::x_SearchMaster(), and CScope_Impl::x_UpdateHandleSeq_id().

CConstRef< CSeq_id > CBioseq_Handle::GetInitialSeqIdOrNull (  void   )  const

Get id used to obtain this bioseq handle. Definition at line 120 of file bioseq_handle.cpp. References GetSeq_id_Handle(), and CSeq_id_Handle::GetSeqIdOrNull().

const CSeq_inst & CBioseq_Handle::GetInst (  void   )  const

Definition at line 204 of file bioseq_handle.cpp. References CBioseq_Info::GetInst(), and x_GetInfo(). Referenced by BOOST_AUTO_TEST_CASE(), MemetoFunctions< CBioseq_EditHandle, CSeq_inst >::Get(), GetNucleotideParent(), CAutoDef::GetOneDefLine(), RemoteFetchLongNucleotideBioseq(), CValidError_imp::ValidateBioSourceForSeq(), x_FindLatestSequence(), CValidError_bioseq::x_IsRangeGap(), and CValidError_bioseq::x_ValidateAbuttingRNA().

const CBioseq_Handle::TInst_Ext & CBioseq_Handle::GetInst_Ext (  void   )  const

Definition at line 360 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Ext(), and x_GetInfo(). Referenced by CMasterContext::CMasterContext(), GetDeltaSeqSummary(), CMasterContext::GetPartNumber(), s_AddPartToSegmentedBioseq(), CBioseqContext::x_IsDeltaLitOnly(), and CMasterContext::x_SetNumParts().

const CBioseq_Handle::TInst_Fuzz & CBioseq_Handle::GetInst_Fuzz (  void   )  const

Definition at line 287 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Fuzz(), and x_GetInfo().

const CBioseq_Handle::TInst_Hist & CBioseq_Handle::GetInst_Hist (  void   )  const

Definition at line 378 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Hist(), and x_GetInfo(). Referenced by GetAllSwitchPoints(), and CPrimaryItem::x_GetStrForPrimary().

CBioseq_Handle::TInst_Length CBioseq_Handle::GetInst_Length (  void   )  const

Definition at line 258 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Length(), and x_GetInfo(). Referenced by CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CValidError_bioseq::CheckForPubOnBioseq(), CAltValidator::GetAccDataFromObjMan(), GetBioseqLength(), GetStop(), s_AddBioseqToBioseq(), s_CDS5primePartialTest(), s_IsLocFullLength(), CValidError_bioseq::ValidateSeqFeatContext(), CAutoDef::x_GetFeatureClauses(), CAsn2FlatApp::x_GetLocation(), CAsn2FastaApp::x_GetLocation(), and CBioseqContext::x_SetLocation().

CBioseq_Handle::TInst_Mol CBioseq_Handle::GetInst_Mol (  void   )  const

Definition at line 240 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Mol(), and x_GetInfo(). Referenced by AddBioseqToBioseq(), CValidError_bioseq::CdError(), CValidError_bioseq::CheckSoureDescriptor(), GetModelEvidance(), GetSequenceType(), CSeqTextDataSource::IsmRNASequence(), s_AddBioseqToBioseq(), s_AddBioseqToNucProtSet(), s_AddProtToNuc(), CValidError_bioseq::ValidateSeqFeatContext(), CBioseqContext::x_Init(), CLocusItem::x_SetStrand(), and CValidError_bioseq::x_ValidateLocusTagGeneralMatch().

CBioseq_Handle::TInst_Repr CBioseq_Handle::GetInst_Repr (  void   )  const

Definition at line 222 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Repr(), and x_GetInfo(). Referenced by GetDeltaSeqSummary(), IsDeltaOrFarSeg(), s_AddPartToSegmentedBioseq(), s_IsSegmented(), s_SeqMapForHandle(), CValidError_bioseq::ValidateSeqFeatContext(), CCleanup_imp::x_ChangeCitSub(), CFlatGatherer::x_DoMultipleSections(), and CBioseqContext::x_GetRepr().

const CBioseq_Handle::TInst_Seq_data & CBioseq_Handle::GetInst_Seq_data (  void   )  const

Definition at line 342 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Seq_data(), and x_GetInfo().

CBioseq_Handle::TInst_Strand CBioseq_Handle::GetInst_Strand (  void   )  const

Definition at line 323 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Strand(), and x_GetInfo(). Referenced by CLocusItem::x_SetStrand().

CBioseq_Handle::TInst_Topology CBioseq_Handle::GetInst_Topology (  void   )  const

Definition at line 305 of file bioseq_handle.cpp. References CBioseq_Info::GetInst_Topology(), and x_GetInfo(). Referenced by CSeqSearch::Search(), CValidError_imp::ValidateSeqLoc(), CLocusItem::x_SetTopology(), and CValidError_bioseq::x_ValidateTitle().

CBioseq_set_Handle CBioseq_Handle::GetParentBioseq_set (  void   )  const

Return a handle for the parent Bioseq-set, or null handle. Definition at line 559 of file bioseq_handle.cpp. References CBioseq_Base_Info::GetParentSeq_entry_Info(), GetTSE_Handle(), CTSE_Info_Object::HasParent_Info(), and x_GetInfo(). Referenced by CSeq_descr_CI::x_Step().

CSeq_entry_Handle CBioseq_Handle::GetParentEntry (  void   )  const

Get parent Seq-entry handle. See also: GetSeq_entry_Handle() Reimplemented in CBioseq_EditHandle. Definition at line 542 of file bioseq_handle.cpp. References GetTSE_Handle(), and x_GetInfo(). Referenced by CRemoveBioseqChecker::Check(), CSeq_annot_CI::CSeq_annot_CI(), CAddBioseqChecker::Do(), CRemoveBioseqChecker::Do(), CFlatFileGenerator::Generate(), GetAssociatedBioSource(), GetComplexityLevel(), GetGenProdSetParent(), CAutoDef::GetMasterLocation(), CSeq_descr_CI::GetSeq_entry_Handle(), GetSeq_entry_Handle(), CFlatFileGenerator::GetSeqFeatText(), CAutoDef::IsSegment(), MakeFullLengthLocation(), CSampleEditSaver::UpdateSeq(), CCleanup_imp::x_ExtendedCleanupMolInfoDescriptors(), CBioseqContext::x_IsPart(), CCleanup_imp::x_RemovePseudoProducts(), and CFlatFeatureRetrieveJob::x_Run().

CRef< CSeq_loc > CBioseq_Handle::GetRangeSeq_loc (  TSeqPos  start, TSeqPos  stop, ENa_strand  strand = eNa_strand_unknown )  const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0, stop == 0, and strand == eNa_strand_unknown, CSeq_loc will be of type 'whole'. Definition at line 976 of file bioseq_handle.cpp. References eNa_strand_unknown, GetAccessSeq_id_Handle(), GetBioseqLength(), CSeq_id_Handle::GetSeqId(), and id. Referenced by s_MakeNewMasterSeq(), and CAnalysisFileLoader::x_CreateSeqGraph().

CSeq_entry_Handle CBioseq_Handle::GetSeq_entry_Handle (  void   )  const

Get parent Seq-entry handle. See also: GetParentEntry() Definition at line 553 of file bioseq_handle.cpp. References GetParentEntry(). Referenced by CCleanup_imp::RemoveEmptyFeaturesDescriptorsAndAnnots(), s_StandaloneProt(), CValidError_bioseq::ValidateBioseq(), CCleanup_imp::x_ConvertOrgFeatToSource(), CCleanupJob::x_CreateProjectItems(), CCleanup_imp::x_MergeAdjacentAnnots(), CCleanup_imp::x_MoveGeneQuals(), CCleanup_imp::x_RecurseForSeqAnnots(), CCleanup_imp::x_RemoveEmptyFeatureAnnots(), CValidError_bioseq::x_ValidateBarcode(), and CValidError_bioseq::x_ValidateMultiplePubs().

CConstRef< CSeq_id > CBioseq_Handle::GetSeqId (  void   )  const

Get id which can be used to access this bioseq handle Throws an exception if none is available. Definition at line 125 of file bioseq_handle.cpp. References GetAccessSeq_id_Handle(), and CSeq_id_Handle::GetSeqId(). Referenced by BOOST_AUTO_TEST_CASE(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CFastaSeqHdrItem::GetAssosiatedObject(), s_AddPartToSegmentedBioseq(), s_CreateKmerCounts(), s_PercentBioseqMatch(), s_TitleFromProtein(), SeqLocToBioseq(), CPromote::x_AddProtFeature(), CGFFFormatter::x_GetGeneID(), CAsn2FlatApp::x_GetLocation(), CAsn2FastaApp::x_GetLocation(), CBioseqContext::x_SetLocation(), and CPromote::x_SetSeqFeatProduct().

const CSeqMap & CBioseq_Handle::GetSeqMap (  void   )  const

Get sequence map. Definition at line 412 of file bioseq_handle.cpp. References CBioseq_Info::GetSeqMap(), and x_GetInfo(). Referenced by ContainsSegment(), CSeqMap_CI::CSeqMap_CI(), GetAllSwitchPoints(), GetBioseqLength(), CBioseq_EditHandle::SetSeqMap(), CFastaOstream::WriteSequence(), CAnnot_Collector::x_Initialize(), and CMasterContext::x_SetBaseName().

CSeqVector CBioseq_Handle::GetSeqVector (  EVectorStrand  strand  )  const

Get sequence. Definition at line 506 of file bioseq_handle.cpp. References eCoding_Ncbi, eNa_strand_minus, eNa_strand_plus, and eStrand_Minus.

CSeqVector CBioseq_Handle::GetSeqVector (  EVectorCoding  coding, EVectorStrand  strand )  const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true. Definition at line 497 of file bioseq_handle.cpp. References eNa_strand_minus, eNa_strand_plus, and eStrand_Minus.

CSeqVector CBioseq_Handle::GetSeqVector (  ENa_strand  strand = eNa_strand_plus  )  const

Get sequence. Definition at line 491 of file bioseq_handle.cpp. References eCoding_Ncbi.

CSeqVector CBioseq_Handle::GetSeqVector (  EVectorCoding  coding, ENa_strand  strand = eNa_strand_plus )  const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true. Definition at line 484 of file bioseq_handle.cpp. Referenced by CValidError_feat::ArePartialsAtSpliceSitesOrGaps(), BOOST_AUTO_TEST_CASE(), GetLoc(), CAlnMixSeq::GetMinusStrandSeqVector(), CAlnMixSeq::GetPlusStrandSeqVector(), GetProteinWeight(), CSeqTextDataSource::GetSeqString(), CSparseAlignment::GetSeqString(), CSimpleOM::GetSeqVector(), RemoteFetchLongNucleotideBioseq(), CSampleObjmgrApplication::Run(), SegMaskerApplication::Run(), CTestTranscript_CountAmbiguities::RunTest(), CTestTranscript_Orfs::RunTest(), CTestTranscript_PolyA::RunTest(), s_GetMaskLoc(), ScanForCpGs(), CSeqSearch::Search(), CGnomonAnnotator_Base::SetGenomic(), CValidError_feat::ValidateCdConflict(), CAnalysisFileLoader::x_CreateSeqGraph(), and CSplign::x_LoadSequence().

CBioseq_Handle::TBioseqStateFlags CBioseq_Handle::GetState (  void   )  const

Get state of the bioseq. May be used with an empty bioseq handle to check why the bioseq retrieval failed. Definition at line 95 of file bioseq_handle.cpp. References CBioseq_ScopeInfo::GetBlobState(), m_Info, and x_GetScopeInfo(). Referenced by State_Confidential(), State_Conflict(), State_Dead(), State_NoData(), State_NotFound(), State_Suppressed(), State_SuppressedPerm(), State_SuppressedTemp(), State_Withdrawn(), and CBuildDatabase::x_AddOneRemoteSequence().

CConstRef< CSynonymsSet > CBioseq_Handle::GetSynonyms (  void   )  const

Get the bioseq's synonyms. Definition at line 514 of file bioseq_handle.cpp. References GetScope(), and CScope::GetSynonyms(). Referenced by ContainsSegment(), CSeq_loc_Mapper::CSeq_loc_Mapper(), and IsSynonym().

CSeq_entry_Handle CBioseq_Handle::GetTopLevelEntry (  void   )  const

Get top level Seq-entry handle. Definition at line 536 of file bioseq_handle.cpp. References GetTSE_Handle(). Referenced by ContainsSegment(), Convert_Seq_id_Bioseq_set(), Convert_Seq_id_Seq_entry(), GetSeqEntryHandle(), IsDeltaOrFarSeg(), CSplitCacheApp::ProcessBlob(), CConversionApp::Read(), CSampleLdsApplication::Run(), CFlatGatherer::x_CollectSourceFeatures(), CDBSourceItem::x_GatherInfo(), and CDeflineGenerator::x_TitleFromNR().

bool CBioseq_Handle::HasAnnots (  void   )  const

Definition at line 384 of file bioseq_handle.cpp. References CBioseq_Base_Info::HasAnnots(), and x_GetInfo().

bool CBioseq_Handle::IsAa (  void   )  const

Definition at line 406 of file bioseq_handle.cpp. References IsProtein(). Referenced by SeqLocToBioseq(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_feat::ValidateImpGbquals(), and CValidError_bioseq::ValidateModifDescriptors().

bool CBioseq_Handle::IsNa (  void   )  const

Definition at line 400 of file bioseq_handle.cpp. References IsNucleotide(). Referenced by s_SeqAlignSetToXMLHsps(), CValidError_feat::ValidateImpGbquals(), CValidError_feat::ValidateNonImpFeat(), and CAlnVecRow::x_GetDescrTooltip().

bool CBioseq_Handle::IsSetDescr (  void   )  const

Definition at line 174 of file bioseq_handle.cpp. References CBioseq_Base_Info::IsSetDescr(), and x_GetInfo(). Referenced by CCleanup_imp::x_ConvertOrgDescToSourceDescriptor(), CCleanup_imp::x_ExtendedCleanupBioSourceDescriptorsAndFeatures(), CCleanup_imp::x_FuseMolInfos(), CCleanup_imp::x_MoveDescriptor(), CCleanup_imp::x_RecurseDescriptorsForMerge(), CCleanup_imp::x_RecurseForDescriptors(), and CCleanup_imp::x_RemoveDescrByType().

bool CBioseq_Handle::IsSetId (  void   )  const

Definition at line 156 of file bioseq_handle.cpp. References CBioseq_Info::IsSetId(), and x_GetInfo(). Referenced by CResetIds_EditCommand::Do(), and CCleanup_imp::x_FixPIDDbtag().

bool CBioseq_Handle::IsSetInst (  void   )  const

Definition at line 192 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst(), and x_GetInfo(). Referenced by GetDeltaSeqSummary(), MemetoFunctions< CBioseq_EditHandle, CSeq_inst >::IsSet(), s_IsSegmented(), s_NsAreGaps(), x_FindLatestSequence(), CBioseqContext::x_Init(), CValidError_bioseq::x_IsRangeGap(), and CValidError_bioseq::x_ValidateAbuttingRNA().

bool CBioseq_Handle::IsSetInst_Ext (  void   )  const

Definition at line 348 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Ext(), and x_GetInfo(). Referenced by GetDeltaSeqSummary(), s_NsAreGaps(), CContigItem::x_GatherInfo(), and CBioseqContext::x_IsDeltaLitOnly().

bool CBioseq_Handle::IsSetInst_Fuzz (  void   )  const

Definition at line 275 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Fuzz(), and x_GetInfo().

bool CBioseq_Handle::IsSetInst_Hist (  void   )  const

Definition at line 366 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Hist(), and x_GetInfo(). Referenced by CFlatGatherer::x_HistoryComments().

bool CBioseq_Handle::IsSetInst_Length (  void   )  const

Definition at line 246 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Length(), and x_GetInfo(). Referenced by GetBioseqLength(), and CValidError_bioseq::ValidateSeqFeatContext().

bool CBioseq_Handle::IsSetInst_Mol (  void   )  const

Definition at line 228 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Mol(), and x_GetInfo(). Referenced by CLocusItem::x_SetStrand().

bool CBioseq_Handle::IsSetInst_Repr (  void   )  const

Definition at line 210 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Repr(), and x_GetInfo(). Referenced by GetDeltaSeqSummary(), IsDeltaOrFarSeg(), s_IsSegmented(), CFlatGatherer::x_DoMultipleSections(), and CBioseqContext::x_GetRepr().

bool CBioseq_Handle::IsSetInst_Seq_data (  void   )  const

Definition at line 329 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Seq_data(), and x_GetInfo(). Referenced by CFastaOstream::WriteSequence().

bool CBioseq_Handle::IsSetInst_Strand (  void   )  const

Definition at line 311 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Strand(), and x_GetInfo(). Referenced by CLocusItem::x_SetStrand().

bool CBioseq_Handle::IsSetInst_Topology (  void   )  const

Definition at line 293 of file bioseq_handle.cpp. References CBioseq_Info::IsSetInst_Topology(), and x_GetInfo().

bool CBioseq_Handle::IsSynonym (  const CSeq_id_Handle &  idh  )  const

Definition at line 529 of file bioseq_handle.cpp. References GetSynonyms().

bool CBioseq_Handle::IsSynonym (  const CSeq_id &  id  )  const

Check if this id can be used to obtain this bioseq handle. Definition at line 523 of file bioseq_handle.cpp. References CSeq_id_Handle::GetHandle(). Referenced by CFlatSeqLoc::x_AddID().

CRef< CSeq_loc > CBioseq_Handle::MapLocation (  const CSeq_loc &  loc  )  const

Map a seq-loc from the bioseq's segment to the bioseq. Definition at line 617 of file bioseq_handle.cpp. References CSeq_loc_Mapper::eSeqMap_Up, and CSeq_loc_Mapper_Base::Map().

void CBioseq_Handle::Reset (  void   )

Reset handle and make it not to point to any bioseq. Definition at line 88 of file bioseq_handle.cpp. References m_Handle_Seq_id, m_Info, CSeq_id_Handle::Reset(), and CScopeInfo_Ref< Info >::Reset(). Referenced by CSelectFeatureDlg::OnButtonLoadFile(), CBioseq_CI::x_Settle(), and CSeq_descr_CI::x_Step().

const CBioseq_Info & CBioseq_Handle::x_GetInfo (  void   )  const

Reimplemented in CBioseq_EditHandle. Definition at line 114 of file bioseq_handle.cpp. References m_Info. Referenced by CanGetDescr(), CanGetId(), CanGetInst(), CanGetInst_Ext(), CanGetInst_Fuzz(), CanGetInst_Hist(), CanGetInst_Length(), CanGetInst_Mol(), CanGetInst_Repr(), CanGetInst_Seq_data(), CanGetInst_Strand(), CanGetInst_Topology(), CSeq_entry_EditHandle::CopySeq(), CSeq_descr_CI::CSeq_descr_CI(), GetBioObjectId(), GetBioseqCore(), GetCompleteBioseq(), GetDescr(), GetFeatureFetchPolicy(), GetId(), GetInst(), GetInst_Ext(), GetInst_Fuzz(), GetInst_Hist(), GetInst_Length(), GetInst_Mol(), GetInst_Repr(), GetInst_Seq_data(), GetInst_Strand(), GetInst_Topology(), GetParentBioseq_set(), GetParentEntry(), GetSeqMap(), HasAnnots(), IsSetDescr(), IsSetId(), IsSetInst(), IsSetInst_Ext(), IsSetInst_Fuzz(), IsSetInst_Hist(), IsSetInst_Length(), IsSetInst_Mol(), IsSetInst_Repr(), IsSetInst_Seq_data(), IsSetInst_Strand(), IsSetInst_Topology(), CBioseq_EditHandle::x_GetInfo(), and CScope_Impl::x_UpdateHandleSeq_id().

const CBioseq_ScopeInfo & CBioseq_Handle::x_GetScopeInfo (  void   )  const [protected]

Reimplemented in CBioseq_EditHandle. Definition at line 108 of file bioseq_handle.cpp. References m_Info. Referenced by GetState(), CScope_Impl::GetSynonyms(), CScope_Impl::GetTSESetWithAnnots(), and CBioseq_EditHandle::x_GetScopeInfo().

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Friends And Related Function Documentation

friend class CScope_Impl [friend]

Reimplemented in CBioseq_EditHandle. Definition at line 452 of file bioseq_handle.hpp.

friend class CSeq_entry_EditHandle [friend]

Definition at line 454 of file bioseq_handle.hpp. Referenced by CBioseq_EditHandle::GetParentEntry().

friend class CSynonymsSet [friend]

Definition at line 453 of file bioseq_handle.hpp.

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Member Data Documentation

CSeq_id_Handle CBioseq_Handle::m_Handle_Seq_id [protected]

Definition at line 465 of file bioseq_handle.hpp. Referenced by CScope_Impl::GetBioseqHandle(), GetSeq_id_Handle(), Reset(), and CScope_Impl::x_UpdateHandleSeq_id().

TLock CBioseq_Handle::m_Info [protected]

Definition at line 466 of file bioseq_handle.hpp. Referenced by CScope_Impl::GetBioseqHandle(), GetState(), GetTSE_Handle(), IsRemoved(), operator!=(), operator<(), operator==(), Reset(), CScope_Impl::x_GetBioseqHandle(), x_GetInfo(), x_GetScopeInfo(), and CScope_Impl::x_SelectSeq().

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The documentation for this class was generated from the following files:

• include/objmgr/bioseq_handle.hpp
• src/objmgr/bioseq_handle.cpp

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