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CBioseq_Handle Class Reference

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CBioseq_Handle –. More...

#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< CBioseqTBioseqCore
 Bioseq core – using partially populated CBioseq. More...
 
typedef CBioseq TObject
 Unified interface for templates. More...
 
typedef vector< CSeq_id_HandleTId
 
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...
 
CScopeGetScope (void) const
 Get scope this handle belongs to. More...
 
CConstRef< CSeq_idGetSeqId (void) const
 Get id which can be used to access this bioseq handle Throws an exception if none is available. More...
 
CConstRef< CSeq_idGetInitialSeqIdOrNull (void) const
 Get id used to obtain this bioseq handle. More...
 
CConstRef< CSeq_idGetNonLocalIdOrNull (void) const
 Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are local. More...
 
CConstRef< CSeq_idGetLocalIdOrNull (void) const
 
const CBioObjectIdGetBioObjectId (void) const
 Get unique object id. More...
 
const CSeq_id_HandleGetSeq_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< CSynonymsSetGetSynonyms (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< CBioseqGetCompleteBioseq (void) const
 Get the complete bioseq. More...
 
CConstRef< TObjectGetCompleteObject (void) const
 
CConstRef< TObjectGetObjectCore (void) const
 
bool IsSetId (void) const
 
bool CanGetId (void) const
 
const TIdGetId (void) const
 
bool IsSetDescr (void) const
 
bool CanGetDescr (void) const
 
const TDescrGetDescr (void) const
 
bool IsSetInst (void) const
 
bool CanGetInst (void) const
 
const TInstGetInst (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_FuzzGetInst_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_dataGetInst_Seq_data (void) const
 
bool IsSetInst_Ext (void) const
 
bool CanGetInst_Ext (void) const
 
const TInst_ExtGetInst_Ext (void) const
 
bool IsSetInst_Hist (void) const
 
bool CanGetInst_Hist (void) const
 
const TInst_HistGetInst_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 CSeqMapGetSeqMap (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_locGetRangeSeq_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_locMapLocation (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_HandleGetTSE_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_Infox_GetInfo (void) const
 

Protected Types

typedef CBioseq_ScopeInfo TScopeInfo
 
typedef CScopeInfo_Ref< TScopeInfoTLock
 

Protected Member Functions

 CBioseq_Handle (const CSeq_id_Handle &id, const TScopeInfo &info)
 
 CBioseq_Handle (const CSeq_id_Handle &id, const TLock &lock)
 
CScope_Implx_GetScopeImpl (void) const
 
const CBioseq_ScopeInfox_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:
Modified on Wed Apr 24 14:11:10 2024 by modify_doxy.py rev. 669887