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| CBioseq_EditHandle (void) |
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| CBioseq_EditHandle (const CBioseq_Handle &h) |
| create edit interface class to the object which already allows editing throw an exception if the argument is not in editing mode More...
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CSeq_entry_EditHandle | GetParentEntry (void) const |
| Navigate object tree. More...
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void | ResetId (void) const |
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bool | AddId (const CSeq_id_Handle &id) const |
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bool | RemoveId (const CSeq_id_Handle &id) const |
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void | ResetDescr (void) const |
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void | SetDescr (TDescr &v) const |
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TDescr & | SetDescr (void) const |
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bool | AddSeqdesc (CSeqdesc &d) const |
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CRef< CSeqdesc > | RemoveSeqdesc (const CSeqdesc &d) const |
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CRef< CSeqdesc > | ReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc) const |
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void | AddSeq_descr (TDescr &v) const |
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void | SetInst (TInst &v) const |
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void | SetInst_Repr (TInst_Repr v) const |
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void | SetInst_Mol (TInst_Mol v) const |
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void | SetInst_Length (TInst_Length v) const |
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void | SetInst_Fuzz (TInst_Fuzz &v) const |
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void | SetInst_Topology (TInst_Topology v) const |
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void | SetInst_Strand (TInst_Strand v) const |
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void | SetInst_Seq_data (TInst_Seq_data &v) const |
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void | SetInst_Ext (TInst_Ext &v) const |
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void | SetInst_Hist (TInst_Hist &v) const |
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CSeq_annot_EditHandle | AttachAnnot (CSeq_annot &annot) const |
| Attach an annotation. More...
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CSeq_annot_EditHandle | CopyAnnot (const CSeq_annot_Handle &annot) const |
| Attach a copy of the annotation. More...
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CSeq_annot_EditHandle | TakeAnnot (const CSeq_annot_EditHandle &annot) const |
| Remove the annotation from its location and attach to current one. More...
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CBioseq_EditHandle | MoveTo (const CSeq_entry_EditHandle &entry, int index=-1) const |
| Move current bioseq into seq-entry. More...
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CBioseq_EditHandle | MoveTo (const CBioseq_set_EditHandle &seqset, int index=-1) const |
| Move current bioseq into seqset. More...
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CBioseq_EditHandle | MoveToSeq (const CSeq_entry_EditHandle &entry) const |
| Move current bioseq into seq-entry and set seq-entry as bioseq. More...
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void | Remove (ERemoveMode mode=eRemoveSeq_entry) const |
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CSeqMap & | SetSeqMap (void) const |
| Get CSeqMap object for sequence editing. More...
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CBioseq_ScopeInfo & | x_GetScopeInfo (void) const |
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CBioseq_Info & | x_GetInfo (void) const |
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void | x_RealResetDescr (void) const |
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void | x_RealSetDescr (TDescr &v) const |
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bool | x_RealAddSeqdesc (CSeqdesc &d) const |
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CRef< CSeqdesc > | x_RealRemoveSeqdesc (const CSeqdesc &d) const |
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CRef< CSeqdesc > | x_RealReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc) const |
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void | x_RealAddSeq_descr (TDescr &v) const |
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void | x_RealResetId (void) const |
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bool | x_RealAddId (const CSeq_id_Handle &id) const |
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bool | x_RealRemoveId (const CSeq_id_Handle &id) const |
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void | x_RealSetInst (TInst &v) const |
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void | x_RealSetInst_Repr (TInst_Repr v) const |
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void | x_RealSetInst_Mol (TInst_Mol v) const |
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void | x_RealSetInst_Length (TInst_Length v) const |
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void | x_RealSetInst_Fuzz (TInst_Fuzz &v) const |
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void | x_RealSetInst_Topology (TInst_Topology v) const |
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void | x_RealSetInst_Strand (TInst_Strand v) const |
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void | x_RealSetInst_Seq_data (TInst_Seq_data &v) const |
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void | x_RealSetInst_Ext (TInst_Ext &v) const |
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void | x_RealSetInst_Hist (TInst_Hist &v) const |
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void | x_RealResetInst () const |
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void | x_RealResetInst_Repr () const |
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void | x_RealResetInst_Mol () const |
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void | x_RealResetInst_Length () const |
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void | x_RealResetInst_Fuzz () const |
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void | x_RealResetInst_Topology () const |
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void | x_RealResetInst_Strand () const |
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void | x_RealResetInst_Seq_data () const |
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void | x_RealResetInst_Ext () const |
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void | x_RealResetInst_Hist () const |
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Public Member Functions inherited from CBioseq_Handle |
| CBioseq_Handle (void) |
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void | Reset (void) |
| Reset handle and make it not to point to any bioseq. More...
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CScope & | GetScope (void) const |
| Get scope this handle belongs to. More...
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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...
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CConstRef< CSeq_id > | GetInitialSeqIdOrNull (void) const |
| Get id used to obtain this bioseq handle. More...
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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...
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CConstRef< CSeq_id > | GetLocalIdOrNull (void) const |
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const CBioObjectId & | GetBioObjectId (void) const |
| Get unique object id. More...
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const CSeq_id_Handle & | GetSeq_id_Handle (void) const |
| Get handle of id used to obtain this bioseq handle. More...
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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...
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TBioseqStateFlags | GetState (void) const |
| Get state of the bioseq. More...
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bool | State_SuppressedTemp (void) const |
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bool | State_SuppressedPerm (void) const |
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bool | State_Suppressed (void) const |
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bool | State_Confidential (void) const |
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bool | State_Dead (void) const |
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bool | State_Withdrawn (void) const |
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bool | State_NoData (void) const |
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bool | State_Conflict (void) const |
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bool | State_NotFound (void) const |
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bool | IsSynonym (const CSeq_id &id) const |
| Check if this id can be used to obtain this bioseq handle. More...
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bool | IsSynonym (const CSeq_id_Handle &idh) const |
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CConstRef< CSynonymsSet > | GetSynonyms (void) const |
| Get the bioseq's synonyms. More...
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CSeq_entry_Handle | GetParentEntry (void) const |
| Get parent Seq-entry handle. More...
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CBioseq_set_Handle | GetParentBioseq_set (void) const |
| Return a handle for the parent Bioseq-set, or null handle. More...
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CSeq_entry_Handle | GetSeq_entry_Handle (void) const |
| Get parent Seq-entry handle. More...
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CSeq_entry_Handle | GetTopLevelEntry (void) const |
| Get top level Seq-entry handle. More...
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CBioseq_EditHandle | GetEditHandle (void) const |
| Get 'edit' version of handle. More...
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TBioseqCore | GetBioseqCore (void) const |
| Get bioseq core structure. More...
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CConstRef< CBioseq > | GetCompleteBioseq (void) const |
| Get the complete bioseq. More...
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CConstRef< TObject > | GetCompleteObject (void) const |
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CConstRef< TObject > | GetObjectCore (void) const |
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bool | IsSetId (void) const |
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bool | CanGetId (void) const |
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const TId & | GetId (void) const |
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bool | IsSetDescr (void) const |
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bool | CanGetDescr (void) const |
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const TDescr & | GetDescr (void) const |
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bool | IsSetInst (void) const |
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bool | CanGetInst (void) const |
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const TInst & | GetInst (void) const |
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bool | IsSetInst_Repr (void) const |
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bool | CanGetInst_Repr (void) const |
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TInst_Repr | GetInst_Repr (void) const |
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bool | IsSetInst_Mol (void) const |
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bool | CanGetInst_Mol (void) const |
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TInst_Mol | GetInst_Mol (void) const |
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bool | IsSetInst_Length (void) const |
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bool | CanGetInst_Length (void) const |
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TInst_Length | GetInst_Length (void) const |
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TSeqPos | GetBioseqLength (void) const |
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bool | IsSetInst_Fuzz (void) const |
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bool | CanGetInst_Fuzz (void) const |
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const TInst_Fuzz & | GetInst_Fuzz (void) const |
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bool | IsSetInst_Topology (void) const |
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bool | CanGetInst_Topology (void) const |
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TInst_Topology | GetInst_Topology (void) const |
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bool | IsSetInst_Strand (void) const |
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bool | CanGetInst_Strand (void) const |
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TInst_Strand | GetInst_Strand (void) const |
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bool | IsSetInst_Seq_data (void) const |
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bool | CanGetInst_Seq_data (void) const |
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const TInst_Seq_data & | GetInst_Seq_data (void) const |
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bool | IsSetInst_Ext (void) const |
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bool | CanGetInst_Ext (void) const |
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const TInst_Ext & | GetInst_Ext (void) const |
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bool | IsSetInst_Hist (void) const |
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bool | CanGetInst_Hist (void) const |
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const TInst_Hist & | GetInst_Hist (void) const |
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bool | HasAnnots (void) const |
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TMol | GetSequenceType (void) const |
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bool | IsProtein (void) const |
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bool | IsNucleotide (void) const |
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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...
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CSeq_entry_Handle | GetExactComplexityLevel (CBioseq_set::EClass cls) const |
| Return level with exact complexity, or empty handle if not found. More...
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TMol | GetBioseqMolType (void) const |
| Get some values from core: More...
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bool | IsNa (void) const |
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bool | IsAa (void) const |
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ESequenceClass | GetSequenceClass (void) const |
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const CSeqMap & | GetSeqMap (void) const |
| Get sequence map. More...
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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...
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bool | ContainsSegment (CSeq_id_Handle id, size_t resolve_depth=kMax_Int, EFindSegment limit_flag=eFindSegment_NoLimit) const |
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bool | ContainsSegment (const CBioseq_Handle &part, size_t resolve_depth=kMax_Int, EFindSegment limit_flag=eFindSegment_NoLimit) const |
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CSeqVector | GetSeqVector (EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const |
| Get sequence: Iupacna or Iupacaa if use_iupac_coding is true. More...
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CSeqVector | GetSeqVector (ENa_strand strand=eNa_strand_plus) const |
| Get sequence. More...
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CSeqVector | GetSeqVector (EVectorCoding coding, EVectorStrand strand) const |
| Get sequence: Iupacna or Iupacaa if use_iupac_coding is true. More...
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CSeqVector | GetSeqVector (EVectorStrand strand) const |
| Get sequence. More...
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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...
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CRef< CSeq_loc > | MapLocation (const CSeq_loc &loc) const |
| Map a seq-loc from the bioseq's segment to the bioseq. More...
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bool | operator== (const CBioseq_Handle &h) const |
| Check if handles point to the same bioseq. More...
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bool | operator!= (const CBioseq_Handle &h) const |
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bool | operator< (const CBioseq_Handle &h) const |
| For usage in containers. More...
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| DECLARE_OPERATOR_BOOL (m_Info.IsValid()) |
| Check if handle points to a bioseq and is not removed. More...
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bool | IsRemoved (void) const |
| Check if handle points to a removed bioseq. More...
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const CTSE_Handle & | GetTSE_Handle (void) const |
| Get CTSE_Handle of containing TSE. More...
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CBioseq_EditHandle | CopyTo (const CSeq_entry_EditHandle &entry, int index=-1) const |
| Copy current bioseq into seq-entry. More...
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CBioseq_EditHandle | CopyTo (const CBioseq_set_EditHandle &seqset, int index=-1) const |
| Copy current bioseq into seqset. More...
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CBioseq_EditHandle | CopyToSeq (const CSeq_entry_EditHandle &entry) const |
| Copy current bioseq into seq-entry and set seq-entry as bioseq. More...
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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...
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EFeatureFetchPolicy | GetFeatureFetchPolicy (void) const |
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const CBioseq_Info & | x_GetInfo (void) const |
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CBioseq_EditHandle –.
Proxy to access and edit the bioseq data
Definition at line 496 of file bioseq_handle.hpp.