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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bioseq__handle_8hpp_source.html below:

NCBI C++ ToolKit: include/objmgr/bioseq_handle.hpp Source File

1 #ifndef BIOSEQ_HANDLE__HPP 2 #define BIOSEQ_HANDLE__HPP 68 class

CSeq_id_ScopeInfo;

129

fState_suppress_temp = 1 << 0,

130

fState_suppress_perm = 1 << 1,

131

fState_suppress = fState_suppress_temp |

132

fState_suppress_perm,

133

fState_dead = 1 << 2,

134

fState_confidential = 1 << 3,

135

fState_withdrawn = 1 << 4,

136

fState_no_data = 1 << 5,

137

fState_conflict = 1 << 6,

138

fState_not_found = 1 << 7,

139

fState_other_error = 1 << 8

146 bool

State_SuppressedTemp(

void

)

const

;

147 bool

State_SuppressedPerm(

void

)

const

;

148 bool

State_Suppressed(

void

)

const

;

149 bool

State_Confidential(

void

)

const

;

150 bool

State_Dead(

void

)

const

;

151 bool

State_Withdrawn(

void

)

const

;

152 bool

State_NoData(

void

)

const

;

153 bool

State_Conflict(

void

)

const

;

154 bool

State_NotFound(

void

)

const

;

157 bool

IsSynonym(

const CSeq_id

id

)

const

;

201 typedef

vector<CSeq_id_Handle>

TId

;

202 bool

IsSetId(

void

)

const

;

203 bool

CanGetId(

void

)

const

;

207 bool

IsSetDescr(

void

)

const

;

208 bool

CanGetDescr(

void

)

const

;

209 const TDescr

& GetDescr(

void

)

const

;

212 bool

IsSetInst(

void

)

const

;

213 bool

CanGetInst(

void

)

const

;

214 const TInst

& GetInst(

void

)

const

;

217 bool

IsSetInst_Repr(

void

)

const

;

218 bool

CanGetInst_Repr(

void

)

const

;

222 bool

IsSetInst_Mol(

void

)

const

;

223 bool

CanGetInst_Mol(

void

)

const

;

227 bool

IsSetInst_Length(

void

)

const

;

228 bool

CanGetInst_Length(

void

)

const

;

230 TSeqPos

GetBioseqLength(

void

)

const

;

233 bool

IsSetInst_Fuzz(

void

)

const

;

234 bool

CanGetInst_Fuzz(

void

)

const

;

235 const TInst_Fuzz

& GetInst_Fuzz(

void

)

const

;

238 bool

IsSetInst_Topology(

void

)

const

;

239 bool

CanGetInst_Topology(

void

)

const

;

243 bool

IsSetInst_Strand(

void

)

const

;

244 bool

CanGetInst_Strand(

void

)

const

;

248 bool

IsSetInst_Seq_data(

void

)

const

;

249 bool

CanGetInst_Seq_data(

void

)

const

;

253 bool

IsSetInst_Ext(

void

)

const

;

254 bool

CanGetInst_Ext(

void

)

const

;

255 const TInst_Ext

& GetInst_Ext(

void

)

const

;

258 bool

IsSetInst_Hist(

void

)

const

;

259 bool

CanGetInst_Hist(

void

)

const

;

260 const TInst_Hist

& GetInst_Hist(

void

)

const

;

262 bool

HasAnnots(

void

)

const

;

267 bool

IsProtein(

void

)

const

;

268 bool

IsNucleotide(

void

)

const

;

302 TMol

GetBioseqMolType(

void

)

const

;

303 bool

IsNa(

void

)

const

;

304 bool

IsAa(

void

)

const

;

312

ESequenceClass GetSequenceClass(

void

)

const

;

315 const CSeqMap

& GetSeqMap(

void

)

const

;

320

eFindSegment_LimitTSE

336 bool

ContainsSegment(

const CSeq_id

id

338

EFindSegment limit_flag = eFindSegment_NoLimit)

const

;

341

EFindSegment limit_flag = eFindSegment_NoLimit)

const

;

344

EFindSegment limit_flag = eFindSegment_NoLimit)

const

;

363 CSeqVector

GetSeqVector(EVectorCoding coding, EVectorStrand strand)

const

;

365 CSeqVector

GetSeqVector(EVectorStrand strand)

const

;

402 bool

IsRemoved(

void

)

const

;

421 int

index = -1)

const

;

434 int

index = -1)

const

;

461

eFeatureFetchPolicy_default = 0,

462

eFeatureFetchPolicy_only_near = 1,

463

eFeatureFetchPolicy_allow_far = 2

465

EFeatureFetchPolicy GetFeatureFetchPolicy(

void

)

const

;

512 void

ResetId(

void

)

const

;

516 void

ResetDescr(

void

)

const

;

517 void

SetDescr(

TDescr

& v)

const

;

518 TDescr

& SetDescr(

void

)

const

;

519 bool

AddSeqdesc(

CSeqdesc

& d)

const

;

522 void

AddSeq_descr(

TDescr

& v)

const

;

524 void

SetInst(

TInst

& v)

const

;

601 int

index = -1)

const

;

614 int

index = -1)

const

;

630 void

Remove(ERemoveMode

mode

= eRemoveSeq_entry)

const

;

633 CSeqMap

& SetSeqMap(

void

)

const

;

641 void

x_Detach(

void

)

const

;

648 void

x_RealResetDescr(

void

)

const

;

649 void

x_RealSetDescr(

TDescr

& v)

const

;

650 bool

x_RealAddSeqdesc(

CSeqdesc

& d)

const

;

653 void

x_RealAddSeq_descr(

TDescr

& v)

const

;

655 void

x_RealResetId(

void

)

const

;

659 void

x_RealSetInst(

TInst

& v)

const

;

660 void

x_RealSetInst_Repr(

TInst_Repr

const

;

661 void

x_RealSetInst_Mol(

TInst_Mol

const

;

663 void

x_RealSetInst_Fuzz(

TInst_Fuzz

& v)

const

;

667 void

x_RealSetInst_Ext(

TInst_Ext

& v)

const

;

668 void

x_RealSetInst_Hist(

TInst_Hist

& v)

const

;

669 void

x_RealResetInst()

const

;

670 void

x_RealResetInst_Repr()

const

;

671 void

x_RealResetInst_Mol()

const

;

672 void

x_RealResetInst_Length()

const

;

673 void

x_RealResetInst_Fuzz()

const

;

674 void

x_RealResetInst_Topology()

const

;

675 void

x_RealResetInst_Strand()

const

;

676 void

x_RealResetInst_Seq_data()

const

;

677 void

x_RealResetInst_Ext()

const

;

678 void

x_RealResetInst_Hist()

const

;

static CSeq_entry_Handle GetSeq_entry_Handle(TTypeInfo type, TConstObjectPtr ptr, CScope &scope)

CBioseq_set_EditHandle â.

bool IsDetached(void) const

const CTSE_Handle & GetTSE_Handle(void) const

friend class CBioseq_EditHandle

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

CScope_Impl & x_GetScopeImpl(void) const

CScope & GetScope(void) const

Returns scope.

Include a standard set of the NCBI C++ Toolkit most basic headers.

bool operator<(const CEquivRange &A, const CEquivRange &B)

bool operator==(const CEquivRange &A, const CEquivRange &B)

unsigned int TSeqPos

Type for sequence locations and lengths.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

DECLARE_OPERATOR_BOOL(m_Info.IsValid())

Check if handle points to a bioseq and is not removed.

TInst::TSeq_data TInst_Seq_data

vector< CSeq_id_Handle > TId

CConstRef< CSeq_id > GetLocalIdOrNull(void) const

bool IsNucleotide(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

TScopeInfo & x_GetScopeInfo(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

bool State_NotFound(void) const

TBioseqStateFlags GetState(void) const

Get state of the bioseq.

TInst::TStrand TInst_Strand

CBioseq_ScopeInfo TScopeInfo

EBioseqStateFlags

State of bioseq handle.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

EFindSegment

Segment search flags.

CConstRef< TObject > GetCompleteObject(void) const

CScope_Impl & x_GetScopeImpl(void) const

CBioseq_Info & x_GetInfo(void) const

friend class CBioseq_Handle

bool State_Conflict(void) const

CConstRef< CBioseq > TBioseqCore

Bioseq core â using partially populated CBioseq.

bool State_NoData(void) const

CBioseq TObject

Unified interface for templates.

TInst::TLength TInst_Length

const CSeq_id_Handle & GetSeq_id_Handle(void) const

Get handle of id used to obtain this bioseq handle.

TInst_Mol GetInst_Mol(void) const

bool State_Dead(void) const

const CBioseq_ScopeInfo & x_GetScopeInfo(void) const

EFeatureFetchPolicy

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

bool operator==(const CBioseq_Handle &h) const

Check if handles point to the same bioseq.

EVectorCoding

CSeqVector constructor flags.

bool IsRemoved(void) const

Check if handle points to a removed bioseq.

bool IsProtein(void) const

CSeq_id_Handle m_Handle_Seq_id

bool State_SuppressedTemp(void) const

CConstRef< TObject > GetObjectCore(void) const

bool State_SuppressedPerm(void) const

CConstRef< CSeq_id > GetNonLocalIdOrNull(void) const

Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are l...

CScopeInfo_Ref< TScopeInfo > TLock

TMol GetSequenceType(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

TInst::TTopology TInst_Topology

bool State_Suppressed(void) const

ERemoveMode

Remove current bioseq from its location.

const CBioseq_Info & x_GetInfo(void) const

bool operator<(const CBioseq_Handle &h) const

For usage in containers.

bool State_Confidential(void) const

CSeq_entry_Info & x_GetInfo(void) const

CBioseq_ScopeInfo & x_GetScopeInfo(void) const

CScope_Impl & x_GetScopeImpl(void) const

bool operator!=(const CBioseq_Handle &h) const

bool State_Withdrawn(void) const

@ eFindSegment_NoLimit

No limit on resolving seq-map.

@ eStrand_Plus

Plus strand.

@ eCoding_NotSet

Use original coding - DANGEROUS! - may change.

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

TObjectType & GetObject(void)

Get object.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

#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.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

#define NCBI_XOBJMGR_EXPORT

ENa_strand

strand of nucleic acid

ERepr

representation class

ETopology

topology of molecule

EMol

molecule class in living organism

EStrand

strandedness in living organism

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

Return a (corrected) set of flags identifying the sequence type.

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