Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/objmgr_2bioseq__info_8cpp_source.html below:

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

: m_AssemblyChunk(-1),

m_FeatureFetchPolicy(-1),

m_Seq_dataChunks(

.m_Seq_dataChunks),

m_AssemblyChunk(

.m_AssemblyChunk),

m_FeatureFetchPolicy(

.m_FeatureFetchPolicy),

.x_UpdateComplete();

ds.

(obj,

);

( !

.IsStr() ||

.GetStr() !=

) {

( !fid.

() || fid.

() !=

) {

(

==

) {

(

==

) {

( policy == -1 ) {

(

.m_SeqMap ) {

(

.IsSetAnnot() ) {

obj->SetId() = src.

();

obj->SetMol(src.

());

find(

.begin(),

.end(),

) !=

.end();

TId::iterator found = find(

.begin(),

.end(),

);

( found !=

.end() ) {

.push_back(

);

->SetId().push_back(seq_id);

TId::iterator found = find(

.begin(),

.end(),

);

( found ==

.end() ) {

->GetInst().GetRepr();

->GetInst().GetMol();

->GetInst().GetLength();

->GetInst().GetFuzz();

->GetInst().GetTopology();

->SetInst().SetTopology(v);

->SetInst().ResetTopology();

->GetInst().GetStrand();

inst.IsSetSeq_data() ||

->GetInst().GetSeq_data();

->SetInst().SetSeq_data(v);

->SetInst().ResetSeq_data();

->GetInst().GetExt();

->GetInst().GetHist();

->GetInst().GetHist().GetAssembly();

->SetInst().SetHist().SetAssembly() = v;

->GetInst().GetHist().GetReplaces();

->SetInst().SetHist().SetReplaces(v);

->GetInst().GetHist().IsSetReplaced_by();

->GetInst().GetHist().CanGetReplaced_by();

->GetInst().GetHist().GetReplaced_by();

->SetInst().SetHist().SetReplaced_by(v);

->GetInst().GetHist().GetDeleted();

->SetInst().SetHist().SetDeleted(v);

);

);

);

ret += (*it)->GetLength();

( seq_loc.

() ) {

);

( delta_seq.

() ) {

);

( it !=

.begin() )

os << it->AsString();

);

org_ref = &desc_src->GetSource().GetOrg();

org_ref = &desc_org->GetOrg();

( it->Which() ) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool IsSetDescr(void) const

TDescList::const_iterator TDesc_CI

virtual void x_ParentAttach(CSeq_entry_Info &parent)

const CSeqdesc * x_SearchFirstDesc(TDescTypeMask type) const

virtual void x_TSEAttachContents(CTSE_Info &tse)

virtual void x_TSEDetachContents(CTSE_Info &tse)

TDesc_CI x_GetFirstDesc(TDescTypeMask types) const

virtual void x_ParentDetach(CSeq_entry_Info &parent)

virtual void x_DSDetachContents(CDataSource &ds)

void x_DoUpdate(TNeedUpdateFlags flags)

virtual void x_DSAttachContents(CDataSource &ds)

bool x_IsEndDesc(TDesc_CI iter) const

TDesc_CI x_GetNextDesc(TDesc_CI iter, TDescTypeMask types) const

bool x_CanGetDescr(void) const

bool CanGetId(void) const

TInst_Mol GetInst_Mol(void) const

const TInst_Fuzz & GetInst_Fuzz(void) const

TInst::THist::TReplaces TInst_Hist_Replaces

void x_ResetObjAnnot(void)

bool CanGetInst_Hist_Replaced_by(void) const

const TInst_Hist_Assembly & GetInst_Hist_Assembly(void) const

bool CanGetInst_Hist(void) const

void x_DoUpdate(TNeedUpdateFlags flags)

bool IsSetInst_Fuzz(void) const

bool CanGetInst_Strand(void) const

bool HasId(const CSeq_id_Handle &id) const

void SetInst_Length(TInst_Length v)

bool CanGetInst_Seq_data(void) const

TObjAnnot & x_SetObjAnnot(void)

TInst_Topology GetInst_Topology(void) const

bool CanGetInst_Repr(void) const

void x_DSDetachContents(CDataSource &ds)

bool RemoveId(const CSeq_id_Handle &id)

TInst_Repr GetInst_Repr(void) const

bool IsSetInst_Hist_Replaced_by(void) const

void x_TSEDetachContents(CTSE_Info &tse)

int GetFeatureFetchPolicy(void) const

int GetSequenceClass(void) const

const TDescr & x_GetDescr(void) const

bool CanGetInst(void) const

vector< CSeq_id_Handle > TId

const CSeqMap & GetSeqMap(void) const

bool IsSetInst_Hist_Deleted(void) const

void SetInst_Hist_Assembly(const TInst_Hist_Assembly &v)

bool IsSetInst_Ext(void) const

bool IsSetInst_Seq_data(void) const

TChunkIds m_Seq_dataChunks

bool x_IsSetDescr(void) const

TTaxId GetTaxId(void) const

bool IsSetInst_Topology(void) const

TInst::THist::TAssembly TInst_Hist_Assembly

void SetInst_Seq_data(TInst_Seq_data &v)

const TId & GetId(void) const

void x_AddAssemblyChunkId(TChunkId chunk_id)

void SetInst_Mol(TInst_Mol v)

static CRef< TObject > sx_ShallowCopy(const TObject &obj)

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)

TDescr & x_SetDescr(void)

void SetInst_Ext(TInst_Ext &v)

bool IsSetInst_Hist_Assembly(void) const

void SetInst_Hist(TInst_Hist &v)

void x_ParentDetach(CSeq_entry_Info &parent)

void SetInst_Strand(TInst_Strand v)

const TInst_Hist_Replaced_by & GetInst_Hist_Replaced_by(void) const

void x_TSEAttachContents(CTSE_Info &tse)

const TInst_Hist & GetInst_Hist(void) const

TInst_Length GetInst_Length(void) const

bool CanGetInst_Hist_Deleted(void) const

bool CanGetInst_Hist_Assembly(void) const

void x_ParentAttach(CSeq_entry_Info &parent)

bool IsSetInst_Repr(void) const

CBioseq_Info(const CBioseq_Info &src, TObjectCopyMap *copy_map)

bool IsSetInst_Mol(void) const

TSeqPos GetBioseqLength(void) const

void SetInst_Repr(TInst_Repr v)

const TInst_Hist_Deleted & GetInst_Hist_Deleted(void) const

string IdString(void) const

bool CanGetInst_Mol(void) const

void x_AddSeq_dataChunkId(TChunkId chunk_id)

bool IsSetInst_Hist(void) const

bool CanGetInst_Hist_Replaces(void) const

const TInst_Hist_Replaces & GetInst_Hist_Replaces(void) const

void ResetInst_Seq_data()

bool CanGetInst_Topology(void) const

void ResetInst_Topology()

bool AddId(const CSeq_id_Handle &id)

bool CanGetInst_Length(void) const

TInst::TLength TInst_Length

CConstRef< TObject > GetBioseqCore(void) const

TInst::THist::TReplaced_by TInst_Hist_Replaced_by

bool IsSetInst_Length(void) const

TInst_Strand GetInst_Strand(void) const

void SetInst_Hist_Replaced_by(TInst_Hist_Replaced_by &v)

void x_DSUnmapObject(CConstRef< TObject > obj, CDataSource &ds)

const TInst_Ext & GetInst_Ext(void) const

void x_SetChangedSeqMap(void)

const TInst & GetInst(void) const

virtual ~CBioseq_Info(void)

TSeqPos x_CalcBioseqLength(void) const

bool IsSetInst_Hist_Replaces(void) const

atomic< int > m_IdChangeCounter

bool IsSetInst(void) const

bool CanGetInst_Fuzz(void) const

void SetInst_Hist_Replaces(TInst_Hist_Replaces &v)

void SetInst_Fuzz(TInst_Fuzz &v)

void SetInst_Hist_Deleted(TInst_Hist_Deleted &v)

bool CanGetInst_Ext(void) const

void x_DSAttachContents(CDataSource &ds)

void x_AttachMap(CSeqMap &seq_map)

void x_DSMapObject(CConstRef< TObject > obj, CDataSource &ds)

void x_SetObject(TObject &obj)

TInst::THist::TDeleted TInst_Hist_Deleted

void x_Unmap(const CObject *obj, const CTSE_Info_Object *info)

void x_Map(const CObject *obj, const CTSE_Info_Object *info)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Base class for all object manager exceptions.

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

TObject & x_GetObject(void)

void ParentizeOneLevel(void)

TSeqPos GetLength(void) const

void x_UpdateCore(void) const

virtual void SetBioObjectId(const CBioObjectId &id)

void x_SetNeedUpdate(TNeedUpdateFlags flags)

CDataSource & GetDataSource(void) const

bool x_NeedUpdate(ENeedUpdate flag) const

void x_Update(TNeedUpdateFlags flags) const

void x_LoadChunks(const TChunkIds &chunk_ids) const

bool HasDataSource(void) const

void x_LoadChunk(TChunkId chunk_id) const

const CTSE_Info & GetTSE_Info(void) const

void x_UpdateComplete(void) const

virtual const CBioObjectId & GetBioObjectId(void) const

CConstRef< CBioseq_Info > FindMatchingBioseq(const CSeq_id_Handle &id) const

CBioObjectId x_IndexBioseq(CBioseq_Info *)

void x_ResetBioseqId(const CSeq_id_Handle &id, CBioseq_Info *info)

void x_SetBioseqId(const CSeq_id_Handle &id, CBioseq_Info *info)

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

@ eFeatureFetchPolicy_default

@ eFeatureFetchPolicy_only_near

@ eFeatureFetchPolicy_allow_far

bool x_UpdateSeq_inst(CSeq_inst &inst)

void SetRepr(CSeq_inst::TRepr repr)

static CRef< CSeqMap > CreateSeqMapForBioseq(const CBioseq &seq)

TSeqPos GetLength(CScope *scope) const

void SetMol(CSeq_inst::TMol mol)

void Reset(void)

Reset reference object.

#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.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

vector< CRef< CUser_field > > TData

list< CRef< CSeq_interval > > Tdata

const Tdata & Get(void) const

Get the member data.

const TWhole & GetWhole(void) const

Get the variant data.

list< CRef< CSeq_loc > > Tdata

E_Choice Which(void) const

Which variant is currently selected.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TEquiv & GetEquiv(void) const

Get the variant data.

list< CRef< CSeq_loc > > Tdata

const TPoints & GetPoints(void) const

Get the Points member data.

const TInt & GetInt(void) const

Get the variant data.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Tpg

Third Party Annot/Seq Genbank.

@ e_not_set

No variant selected.

@ e_Equiv

equivalent sets of locations

@ e_Empty

to NULL one Seq-id in a collection

const TSeq & GetSeq(void) const

Get the variant data.

TRepr GetRepr(void) const

Get the Repr member data.

const TSeg & GetSeg(void) const

Get the variant data.

const TUser & GetUser(void) const

Get the variant data.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

TStrand GetStrand(void) const

Get the Strand member data.

ERepr

representation class

const TInst & GetInst(void) const

Get the Inst member data.

TTopology GetTopology(void) const

Get the Topology member data.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

bool IsSetRepr(void) const

Check if a value has been assigned to Repr data member.

bool IsSetMol(void) const

Check if a value has been assigned to Mol data member.

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

bool IsSetStrand(void) const

Check if a value has been assigned to Strand data member.

const TLiteral & GetLiteral(void) const

Get the variant data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetHist(void) const

sequence history Check if a value has been assigned to Hist data member.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

const Tdata & Get(void) const

Get the member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

TMol GetMol(void) const

Get the Mol member data.

const CSeq_loc & Get(void) const

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

const THist & GetHist(void) const

Get the Hist member data.

const TExt & GetExt(void) const

Get the Ext member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

ETopology

topology of molecule

EMol

molecule class in living organism

E_Choice Which(void) const

Which variant is currently selected.

const TDelta & GetDelta(void) const

Get the variant data.

const TLoc & GetLoc(void) const

Get the variant data.

EStrand

strandedness in living organism

bool IsSetId(void) const

equivalent identifiers Check if a value has been assigned to Id data member.

list< CRef< CSeq_annot > > TAnnot

list< CRef< CDelta_seq > > Tdata

const Tdata & Get(void) const

Get the member data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

list< CRef< CSeq_loc > > Tdata

const TDescr & GetDescr(void) const

Get the Descr member data.

const TRef & GetRef(void) const

Get the variant data.

bool IsSetTopology(void) const

Check if a value has been assigned to Topology data member.

bool IsSetFuzz(void) const

length uncertainty Check if a value has been assigned to Fuzz data member.

bool IsUser(void) const

Check if variant User is selected.

@ e_Seg

segmented sequences

@ e_Ref

hot link to another sequence (a view)

@ e_Org

if all from one organism

@ e_User

user defined object

@ e_Source

source of materials, includes Org-ref

@ e_Literal

a piece of sequence

@ e_Loc

point to a sequence

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is whole

Int4 delta(size_t dimension_, const Int4 *score_)

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

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4