Search Toolkit Book for CBioseq_Handle

#include <objmgr/bioseq_handle.hpp>

Inheritance diagram for CBioseq_Handle:

Collaboration diagram for CBioseq_Handle:

Public Types
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	ESequenceClass { eSequenceClass_none , eSequenceClass_INSD , eSequenceClass_REFSEQ , eSequenceClass_TPA }

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 , eFeatureFetchPolicy_allow_far = 2 }
	Feature fetch policy describes when to look for features on sequence segments. More...

typedef int	TBioseqStateFlags

typedef CConstRef< CBioseq >	TBioseqCore
	Bioseq core – using partially populated CBioseq. More...

typedef CBioseq	TObject
	Unified interface for templates. More...

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

Public Member Functions
	CBioseq_Handle (void)

void	Reset (void)
	Reset handle and make it not to point to any bioseq. More...

CScope &	GetScope (void) const
	Get scope this handle belongs to. More...

CConstRef< CSeq_id >	GetSeqId (void) const
	Get id which can be used to access this bioseq handle Throws an exception if none is available. More...

CConstRef< CSeq_id >	GetInitialSeqIdOrNull (void) const
	Get id used to obtain this bioseq handle. More...

CConstRef< CSeq_id >	GetNonLocalIdOrNull (void) const
	Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are local. More...

CConstRef< CSeq_id >	GetLocalIdOrNull (void) const

const CBioObjectId &	GetBioObjectId (void) const
	Get unique object id. More...

const CSeq_id_Handle &	GetSeq_id_Handle (void) const
	Get handle of id used to obtain this bioseq handle. More...

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. More...

TBioseqStateFlags	GetState (void) const
	Get state of the bioseq. More...

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. More...

bool	IsSynonym (const CSeq_id_Handle &idh) const

CConstRef< CSynonymsSet >	GetSynonyms (void) const
	Get the bioseq's synonyms. More...

CSeq_entry_Handle	GetParentEntry (void) const
	Get parent Seq-entry handle. More...

CBioseq_set_Handle	GetParentBioseq_set (void) const
	Return a handle for the parent Bioseq-set, or null handle. More...

CSeq_entry_Handle	GetSeq_entry_Handle (void) const
	Get parent Seq-entry handle. More...

CSeq_entry_Handle	GetTopLevelEntry (void) const
	Get top level Seq-entry handle. More...

CBioseq_EditHandle	GetEditHandle (void) const
	Get 'edit' version of handle. More...

TBioseqCore	GetBioseqCore (void) const
	Get bioseq core structure. More...

CConstRef< CBioseq >	GetCompleteBioseq (void) const
	Get the complete bioseq. More...

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) More...

CSeq_entry_Handle	GetExactComplexityLevel (CBioseq_set::EClass cls) const
	Return level with exact complexity, or empty handle if not found. More...

TMol	GetBioseqMolType (void) const
	Get some values from core: More...

bool	IsNa (void) const

bool	IsAa (void) const

ESequenceClass	GetSequenceClass (void) const

const CSeqMap &	GetSeqMap (void) const
	Get sequence map. More...

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. More...

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. More...

CSeqVector	GetSeqVector (ENa_strand strand=eNa_strand_plus) const
	Get sequence. More...

CSeqVector	GetSeqVector (EVectorCoding coding, EVectorStrand strand) const
	Get sequence: Iupacna or Iupacaa if use_iupac_coding is true. More...

CSeqVector	GetSeqVector (EVectorStrand strand) const
	Get sequence. More...

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'. More...

CRef< CSeq_loc >	MapLocation (const CSeq_loc &loc) const
	Map a seq-loc from the bioseq's segment to the bioseq. More...

bool	operator== (const CBioseq_Handle &h) const
	Check if handles point to the same bioseq. More...

bool	operator!= (const CBioseq_Handle &h) const

bool	operator< (const CBioseq_Handle &h) const
	For usage in containers. More...

	DECLARE_OPERATOR_BOOL (m_Info.IsValid())
	Check if handle points to a bioseq and is not removed. More...

bool	IsRemoved (void) const
	Check if handle points to a removed bioseq. More...

const CTSE_Handle &	GetTSE_Handle (void) const
	Get CTSE_Handle of containing TSE. More...

CBioseq_EditHandle	CopyTo (const CSeq_entry_EditHandle &entry, int index=-1) const
	Copy current bioseq into seq-entry. More...

CBioseq_EditHandle	CopyTo (const CBioseq_set_EditHandle &seqset, int index=-1) const
	Copy current bioseq into seqset. More...

CBioseq_EditHandle	CopyToSeq (const CSeq_entry_EditHandle &entry) const
	Copy current bioseq into seq-entry and set seq-entry as bioseq. More...

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. More...

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

Detailed Description

CBioseq_Handle –.

Proxy to access the bioseq data

Definition at line 90 of file bioseq_handle.hpp.

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

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

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Friends

Detailed Description