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NCBI C++ ToolKit: src/gui/objutils/object_index.cpp Source File

: m_OriginalAccNoVer(

)

& scope,

product)

: m_OriginalAccNoVer(

)

(obj_handle,

, scope, product);

& scope,

product)

: m_ProductDescr(

)

: m_Original(original),

TIdDescrs::iterator it_id =

(obj_handle,

, product);

&

,

product)

rec(descr,

, product);

vector<CSeq_id_Handle>& handles = descr->

();

(

= 0;

< handles.size();

++ ) {

rec(descr,

, product);

start = 0;

stop = 0;

stop = total_r.

();

(

<< e.

());

res = start ^ ((start - stop) << 16);

= (

)

.GetSubtype();

(

);

product_descr =

(obj_handle, *

,

);

descr->

(obj_handle, feature, product_descr, *

);

(vcf_variant.

(*iter->first)) {

(vcf_variant.

(*iter->first)) {

matching_vcf_variant->second = obj_handle;

type_info&

=

(obj);

(obj_handle, *feature);

(obj_handle, *

);

* loc =

*

(&obj);

(obj_handle, *loc->

);

(obj_handle, *align);

(obj_handle, *vcf_variant);

(

<<

.name());

removed =

;

type_info&

=

(obj);

removed =

(*feature);

removed =

(*align);

removed =

(*vcf_variant);

(

<<

.name());

(descr->

()->Match(

)) {

vector<CSeq_id_Handle> handles = descr->

();

handles.push_back(idh);

(

= 0;

< handles.size();

++ ) {

& rec = it->second;

pair<TCodeToFeatMap::iterator , TCodeToFeatMap::iterator> p =

found_match =

;

(&feat == &feature) {

type_info&

=

(object);

type_info&

=

(object);

vector<CSeq_id_Handle>& handles = descr.

();

(

= 0;

< handles.size();

++ ) {

vector<CSeq_id_Handle>& handles = descr.

();

(

= 0;

< handles.size();

++ ) {

at_least_one,

no_ver)

& rec = it->second;

(at_least_one && (rec.

|| no_ver)) {

& rec = it->second;

(at_least_one && (rec.

|| no_ver)) {

pair<TCodeToFeatMap::const_iterator , TCodeToFeatMap::const_iterator> p =

(feat.

(feature)) {

pair<TCodeToFeatMap::const_iterator , TCodeToFeatMap::const_iterator> p =

(&feat == &feature || feat.

(feature)) {

.insert(matching_vcf_variant->second);

.push_back(TR(vcf_variant));

ids.push_back(descr->

());

features.push_back(feat);

aligns.push_back(align);

@ eExtreme_Positional

numerical value

CConstRef< objects::CSeq_id > m_Id

void Clear(objects::CScope *scope)

TVcfVariantMap::iterator x_FindVcfVariant(const objects::CVcfVariant &vcf_variant)

void x_GetMatches(const CSeq_id_Descr &descr, const objects::CSeq_id_Handle &h, bool at_least_one, bool no_ver, TResults &results) const

bool x_HasMatches(const CSeq_id_Descr &descr, const objects::CSeq_id_Handle &h, bool at_least_one, bool no_ver) const

bool Remove(const CObject &obj)

map< CConstRef< objects::CVcfVariant >, ISelObjectHandle * > TVcfVariantMap

void x_RemoveFromIdMap(const CSeq_id_Descr *descr)

CSeq_id_Descr * x_Add(ISelObjectHandle *obj_handle, const objects::CSeq_id &id, bool product)

void x_Remove(const CSeq_id_Descr *descr)

void GetObjects(TConstObjects &objects) const

TVcfVariantMap m_VcfVariantMap

set< const ISelObjectHandle * > TResults

static TFeatCode x_GetFeatureCode(const objects::CSeq_feat &feature)

bool HasMatches(const CObject &object, objects::CScope &scope) const

void GetAligns(vector< const objects::CSeq_align * > &aligns) const

vector< CSeq_id_Descr * > TIdDescrs

void GetFeatures(vector< const objects::CSeq_feat * > &features) const

void Add(ISelObjectHandle *obj_handle, CObject &obj)

void GetOriginalIds(vector< const objects::CSeq_id * > &ids) const

CRef< objects::CScope > m_Scope

void GetMatches(const CObject &object, objects::CScope &scope, TResults &results) const

static bool sm_MatchByProduct

static EObjMatchPolicy sm_ObjMatchPolicy

static EIdMatchPolicy sm_IdMatchPolicy

CRef< ISelObjectHandle > m_ObjHandle

CSeq_feat_Descr()

CSeq_feat_Descr.

CConstRef< objects::CSeq_feat > m_Feat

void Assign(ISelObjectHandle *obj_handle, const objects::CSeq_feat &feat, CSeq_id_Descr *, objects::CScope &scope)

const CSeq_id_Descr * GetProductDescr() const

CSeq_id_Descr * m_ProductDescr

const CRef< ISelObjectHandle > GetObjectHandle() const

const objects::CSeq_feat & GetFeat() const

namespace ncbi::objects::

CSeq_id_Descr()

CSeq_id_Descr.

CConstRef< objects::CSeq_id > m_Id

bool HasOriginalAccNoVer() const

const objects::CSeq_id_Handle & GetAccNoVer() const

void Assign(ISelObjectHandle *obj_handle, const objects::CSeq_id &id, objects::CScope &scope, bool product=false)

const TIdHandleVector & GetIdHandles() const

CRef< ISelObjectHandle > m_ObjHandle

const objects::CSeq_id * GetId() const

TIdHandleVector m_IdHandles

objects::CSeq_id_Handle m_AccNoVer

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator_pair equal_range(const key_type &key) const

container_type::const_iterator const_iterator

iterator insert(const value_type &val)

container_type::iterator iterator

container_type::value_type value_type

#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.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

const string & GetMsg(void) const

Get message string.

bool WeakMatch(const CVcfVariant &right) const

vector< CConstRef< CObject > > TConstObjects

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

bool HaveMatchingHandles(void) const

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

TSeqPos GetStop(ESeqLocExtremes ext) const

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsSetAccession(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetRelease(void) const

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

bool IsSetVersion(void) const

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

bool IsSetName(void) const

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

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

const TAccession & GetAccession(void) const

Get the Accession member data.

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

const GenericPointer< typename T::ValueType > T2 value

bool IsAccessionNoVersion(const CSeq_id &seq_id)

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

SRec(CSeq_id_Descr *descr, bool original=true, bool product=false)

CObjectIndex.

const CSeq_id_Descr * GetIdDescr() const

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