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NCBI C++ ToolKit: src/objmgr/bioseq_handle.cpp Source File

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CId_EditCommand< true > CAddId_EditCommand

CId_EditCommand< false > CRemoveId_EditCommand

bool IsSetDescr(void) const

bool HasAnnots(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d)

CRef< CSeqdesc > ReplaceSeqdesc(const CSeqdesc &old_desc, CSeqdesc &new_desc)

const TDescr & GetDescr(void) const

void AddSeq_descr(const TDescr &v)

bool AddSeqdesc(CSeqdesc &d)

bool CanGetDescr(void) const

bool CanGetId(void) const

TInst_Mol GetInst_Mol(void) const

const TInst_Fuzz & GetInst_Fuzz(void) const

bool CanGetInst_Hist(void) const

bool IsSetInst_Fuzz(void) const

bool CanGetInst_Strand(void) const

void SetInst_Length(TInst_Length v)

bool CanGetInst_Seq_data(void) const

TInst_Topology GetInst_Topology(void) const

bool CanGetInst_Repr(void) const

TInst_Repr GetInst_Repr(void) const

bool CanGetInst(void) const

const CSeqMap & GetSeqMap(void) const

bool IsSetInst_Ext(void) const

bool IsSetInst_Seq_data(void) const

bool IsSetInst_Topology(void) const

void SetInst_Seq_data(TInst_Seq_data &v)

const TId & GetId(void) const

void SetInst_Mol(TInst_Mol v)

const TInst_Seq_data & GetInst_Seq_data(void) const

bool IsSetInst_Strand(void) const

CConstRef< TObject > GetCompleteBioseq(void) const

void SetInst_Topology(TInst_Topology v)

void SetInst_Ext(TInst_Ext &v)

void SetInst_Hist(TInst_Hist &v)

void SetInst_Strand(TInst_Strand v)

const TInst_Hist & GetInst_Hist(void) const

TInst_Length GetInst_Length(void) const

bool IsSetInst_Repr(void) const

bool IsSetInst_Mol(void) const

void SetInst_Repr(TInst_Repr v)

bool CanGetInst_Mol(void) const

bool IsSetInst_Hist(void) const

void ResetInst_Seq_data()

bool CanGetInst_Topology(void) const

void ResetInst_Topology()

bool CanGetInst_Length(void) const

CConstRef< TObject > GetBioseqCore(void) const

bool IsSetInst_Length(void) const

TInst_Strand GetInst_Strand(void) const

const TInst_Ext & GetInst_Ext(void) const

const TInst & GetInst(void) const

bool IsSetInst(void) const

bool CanGetInst_Fuzz(void) const

void SetInst_Fuzz(TInst_Fuzz &v)

bool CanGetInst_Ext(void) const

TBlobStateFlags GetBlobState(void) const

bool HasBioseq(void) const

bool AddId(const CSeq_id_Handle &id)

bool RemoveId(const CSeq_id_Handle &id)

const CBioseq_Info & GetObjectInfo(void) const

CBioseq_set_EditHandle –.

CMDReturn< CMD >::TReturn run(CMD *cmd)

Base class for all object manager exceptions.

const CTSE_Handle & GetTSE_Handle(void) const

CTSE_Handle GetEditHandle(const CTSE_Handle &src_tse)

@Seq_descr.hpp User-defined methods of the data storage class.

const CBioseq_set_Info & GetParentBioseq_set_Info(void) const

bool AddUsedTSE(const CTSE_Handle &tse) const

Register argument TSE as used by this TSE, so it will be released by scope only after this TSE is rel...

bool CanBeEdited(void) const

Return true if this TSE handle is local to scope and can be edited.

const CTSE_Info & x_GetTSE_Info(void) const

bool HasParent_Info(void) const

virtual const CBioObjectId & GetBioObjectId(void) const

TBlobState GetBlobState(void) const

IEditSaver * GetEditSaver(const Handle &handle)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

CConstRef< CSeq_id > GetSeqId(void) const

void Reset(void)

Reset the handle (remove seq-id reference)

CConstRef< CSeq_id > GetSeqIdOrNull(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id &id)

Get bioseq synonyms, resolving to the bioseq in this scope.

@ eSeqMap_Up

map from segments to the top level bioseq

vector< CSeq_id_Handle > TId

void x_RealResetId(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 ...

void x_RealResetInst_Strand() const

bool IsSetInst_Strand(void) const

bool IsSetInst_Mol(void) const

void x_RealSetInst_Ext(TInst_Ext &v) const

void x_RealResetInst_Ext() const

bool CanGetInst_Repr(void) const

bool IsSetInst_Fuzz(void) const

bool IsNucleotide(void) const

EFeatureFetchPolicy GetFeatureFetchPolicy(void) const

bool AddId(const CSeq_id_Handle &id) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

bool IsSetInst_Seq_data(void) const

const TInst_Hist & GetInst_Hist(void) const

void x_RealResetInst_Topology() const

void x_Detach(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

const TInst_Ext & GetInst_Ext(void) const

TBioseqStateFlags GetState(void) const

Get state of the bioseq.

CSeq_annot_EditHandle TakeAnnot(const CSeq_annot_EditHandle &annot) const

Remove the annotation from its location and attach to current one.

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

void x_RealSetInst_Fuzz(TInst_Fuzz &v) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CConstRef< CSeq_id > GetInitialSeqIdOrNull(void) const

Get id used to obtain this bioseq handle.

bool IsSetInst_Hist(void) const

CBioseq_EditHandle MoveTo(const CSeq_entry_EditHandle &entry, int index=-1) const

Move current bioseq into seq-entry.

bool IsSetInst_Ext(void) const

void x_RealResetInst() const

CBioseq_EditHandle CopyToSeq(const CSeq_entry_EditHandle &entry) const

Copy current bioseq into seq-entry and set seq-entry as bioseq.

EFindSegment

Segment search flags.

CRef< CSeqdesc > x_RealRemoveSeqdesc(const CSeqdesc &d) const

CScope_Impl & x_GetScopeImpl(void) const

void SetInst_Mol(TInst_Mol v) const

void x_RealResetDescr(void) const

CBioseq_Info & x_GetInfo(void) const

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 n...

static const TComplexityTable & sx_GetComplexityTable(void)

bool CanGetInst(void) const

void SetInst_Seq_data(TInst_Seq_data &v) const

TSeqPos GetBioseqLength(void) const

TInst::TLength TInst_Length

bool x_RealAddSeqdesc(CSeqdesc &d) const

void Remove(void) const

Remove this Seq-entry from parent, or scope if it's top level Seq-entry.

const CSeq_id_Handle & GetSeq_id_Handle(void) const

Get handle of id used to obtain this bioseq handle.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

void x_RealResetInst_Hist() const

void SetInst_Length(TInst_Length v) const

void x_RealResetInst_Fuzz() const

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 bios...

TInst_Mol GetInst_Mol(void) const

bool CanGetInst_Length(void) const

void x_RealSetInst_Strand(TInst_Strand v) const

bool HasAnnots(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

const CBioseq_ScopeInfo & x_GetScopeInfo(void) const

EFeatureFetchPolicy

Feature fetch policy describes when to look for features on sequence segments.

void x_RealSetInst_Repr(TInst_Repr v) const

void SetInst(TInst &v) const

void x_RealSetDescr(TDescr &v) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

CRef< CSeqdesc > ReplaceSeqdesc(const CSeqdesc &old_desc, CSeqdesc &new_desc) const

TInst_Strand GetInst_Strand(void) const

bool x_RealAddId(const CSeq_id_Handle &id) const

bool IsSetInst_Length(void) const

EVectorCoding

CSeqVector constructor flags.

bool CanGetInst_Hist(void) const

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

bool IsProtein(void) const

CSeq_id_Handle m_Handle_Seq_id

bool RemoveId(const CSeq_id_Handle &id) const

void SetInst_Repr(TInst_Repr v) const

CBioseq_EditHandle TakeBioseq(const CBioseq_EditHandle &seq, int index=-1) const

Remove bioseq from its location and attach to current one.

TInst_Topology GetInst_Topology(void) const

CBioseq_EditHandle CopyBioseq(const CBioseq_Handle &seq, int index=-1) const

Attach a copy of the bioseq.

bool CanGetInst_Strand(void) const

CSeq_annot_EditHandle CopyAnnot(const CSeq_annot_Handle &annot) const

Attach a copy of the annotation.

const TDescr & GetDescr(void) const

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

Copy current bioseq into seq-entry.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

TInst_Length GetInst_Length(void) const

void x_RealResetInst_Mol() const

void x_RealSetInst(TInst &v) const

CBioseq_EditHandle CopyBioseq(const CBioseq_Handle &seq, int index=-1) const

Attach a copy of the existing bioseq.

TSeq CopySeq(const CBioseq_Handle &seq) const

Make the empty Seq-entry be in seq state with specified Bioseq object.

bool IsSetInst(void) const

void Reset(void)

Reset handle and make it not to point to any bioseq.

bool IsSetInst_Repr(void) const

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 CanGetInst_Topology(void) const

bool IsSetClass(void) const

bool AddSeqdesc(CSeqdesc &d) const

bool CanGetInst_Fuzz(void) const

TMol GetSequenceType(void) const

TInst_Repr GetInst_Repr(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d) const

void x_RealSetInst_Mol(TInst_Mol v) const

void x_RealSetInst_Hist(TInst_Hist &v) const

const CBioObjectId & GetBioObjectId(void) const

Get unique object id.

void x_RealAddSeq_descr(TDescr &v) const

CSeqMap & SetSeqMap(void) const

Get CSeqMap object for sequence editing.

CBioseq_EditHandle TakeBioseq(const CBioseq_EditHandle &seq, int index=-1) const

Remove bioseq from its location and attach to current one.

const TInst_Seq_data & GetInst_Seq_data(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

void SetInst_Strand(TInst_Strand v) const

ERemoveMode

Remove current bioseq from its location.

const CBioseq_Info & x_GetInfo(void) const

void x_RealSetInst_Seq_data(TInst_Seq_data &v) const

bool CanGetId(void) const

void x_RealResetInst_Repr() const

void SetInst_Hist(TInst_Hist &v) const

CSeq_entry_Handle GetExactComplexityLevel(CBioseq_set::EClass cls) const

Return level with exact complexity, or empty handle if not found.

void x_RealResetInst_Length() const

void SetInst_Ext(TInst_Ext &v) const

void AddSeq_descr(TDescr &v) const

void ResetDescr(void) const

CSeq_annot_EditHandle TakeAnnot(const CSeq_annot_EditHandle &annot) const

Remove the annotation from its location and attach to current one.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

bool IsSetDescr(void) const

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,...

friend class CSeq_entry_EditHandle

void SetInst_Fuzz(TInst_Fuzz &v) const

ESequenceClass GetSequenceClass(void) const

CBioseq_ScopeInfo & x_GetScopeInfo(void) const

void x_RealSetInst_Topology(TInst_Topology v) const

void Reset(void)

Reset handle and make it not to point to any seq-entry.

bool IsSetInst_Topology(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TDescr & SetDescr(void) const

CSeq_annot_EditHandle CopyAnnot(const CSeq_annot_Handle &annot) const

Attach a copy of the annotation.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const TId & GetId(void) const

void SetInst_Topology(TInst_Topology v) const

CBioseq_EditHandle MoveToSeq(const CSeq_entry_EditHandle &entry) const

Move current bioseq into seq-entry and set seq-entry as bioseq.

bool CanGetInst_Seq_data(void) const

TSeq TakeSeq(const TSeq &seq) const

Make the empty Seq-entry be in seq state with moving bioseq object from the argument seq.

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

Map a seq-loc from the bioseq's segment to the bioseq.

CSeq_entry_EditHandle GetParentEntry(void) const

Navigate object tree.

bool x_RealRemoveId(const CSeq_id_Handle &id) const

void x_RealSetInst_Length(TInst_Length v) const

CConstRef< CSynonymsSet > GetSynonyms(void) const

Get the bioseq's synonyms.

CRef< CSeqdesc > x_RealReplaceSeqdesc(const CSeqdesc &old_desc, CSeqdesc &new_desc) const

bool CanGetInst_Ext(void) const

bool IsSynonym(const CSeq_id &id) const

Check if this id can be used to obtain this bioseq handle.

TMol GetBioseqMolType(void) const

Get some values from core:

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

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

void x_RealResetInst_Seq_data() const

bool CanGetDescr(void) const

const TInst_Fuzz & GetInst_Fuzz(void) const

bool CanGetInst_Mol(void) const

const TInst & GetInst(void) const

@ eFindSegment_LimitTSE

Resolve in the parent TSE only.

@ eStrand_Minus

Minus strand.

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

SSeqMapSelector & SetLimitTSE(const CSeq_entry_Handle &tse)

Limit TSE to resolve references.

CSeq_id_Handle GetRefSeqid(void) const

The following function makes sense only when the segment is a reference to another seq.

CSeqMap_CI BeginResolved(CScope *scope) const

TSeqPos GetLength(CScope *scope) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

ENa_strand

strand of nucleic acid

ERepr

representation class

ETopology

topology of molecule

EMol

molecule class in living organism

EStrand

strandedness in living organism

Selector used in CSeqMap methods returning iterators.

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