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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/label_8cpp_source.html below:

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

=

;

(item.IsSetItem()) {

item.SetLabel(

);

(type_info != CSeq_id::GetTypeInfo());

(type_info != CSeq_loc::GetTypeInfo());

(type_info != CSeq_entry::GetTypeInfo());

(type_info != CBioseq::GetTypeInfo());

(type_info != CBioseq_set::GetTypeInfo());

iter->second->GetLabel(obj,

,

, scope);

iter->second->GetLabel(obj,

,

, scope);

*

=

+

(

(obj).name()) +

;

length_limit,

length_tolerance)

(!

)

;

(

->empty())

;

(

<= length_limit)

;

point_found =

;

= length_limit;

max_len =

(

,

(length_limit + length_tolerance));

(;

< max_len; ++

) {

c = (*label)[

];

(c ==

|| c ==

) {

( !point_found ) {

(;

< max_len; ++

) {

c = (*label)[

];

(c ==

|| c ==

) {

( !point_found ) {

->append(

);

& user_subtype,

& icon_alias)

= user_type +

+ user_subtype;

= user_type +

+ user_subtype;

}

( ! user_subtype.empty()) {

= user_type +

;

objects::CScope* scope)

, subtype;

*

= it->second;

(; iter != caches.

(); ++iter) {

(

.IsLocal() )

gi;

( (gi ==

) && scope ){

}

( std::exception& ){

( !

->empty() ){

(

->empty() ){

fastaLabel =

.AsFastaString();

( !

.empty() ){

}

(

+ fastaLabel +

);

( scope && id_ptr->

() ){

( !last_id || !interval.

().

(*last_id)) {

( !

->empty() ) {

intervals = 0;

(loc.

()) {

intervals = loc.

().

().size();

(intervals != 0) {

( !extra_info.empty() )

extra_info +=

;

(intervals != 1) {

( !extra_info.empty() ) {

*

+= extra_info;

&

= it.GetSeq_id();

(

= 0;

< locs.size(); ++

) {

(

== locs.size()) {

locs[

]->Add(*it.GetRangeAsSeq_loc());

(loc.

()) {

*

+=

;

*

+=

;

(loc.

()) {

( !

.empty() ) {

.Reset(&ival.

());

.GetPointer();

( !

->empty() ) {

}

( !

->empty() ) {

( !

.empty() ) {

( !

->empty() ) {

}

( !

->empty() ) {

( !

.empty() ) {

vector<CRef<CSeq_loc> > locs;

(

= 0;

< locs.size(); ++

) {

(bioseq->

()) {

}

(bioseq->

()) {

sc_Types[] = {

TBioseq_setTypes::const_iterator

= sc_Bioseq_setTypes.find(bst.

());

*

+= (

!= sc_Bioseq_setTypes.end()) ?

sc_Bioseq_setTypes.find(bst.

())->second :

((*it)->IsSeq()) {

bsp = &(*it)->GetSeq();

}

((*it)->IsSet()) {

(ids.begin(), ids.end());

vector<string>::iterator new_end = unique(ids.begin(), ids.end());

(new_end != ids.end()) {

*

+= ids.front();

(ids.size() > 1) {

*

+= ids.back();

}

(lcl !=

) {

(align_it.

() != 0) {

( !

)

;

(bioseq_set->

()) {

*

+=

.GetStr();

*

+=

.GetStr();

(

.IsStr() &&

.GetStr() ==

) {

*

+=

.GetStr();

field = obj.

(

);

( !

->empty() ) {

*

+=

;

field = obj.

(

);

( !

->empty() ) {

*

+=

;

field = obj.

(

);

( !

->empty() ) {

*

+=

;

}

(

.IsStr() &&

num_str = feat.GetNamedQual(

);

( !num_str.empty() ) {

((*iter)->IsLoss_of_heterozygosity()) {

*

+=

;

*

+=

;

(product_str != type_str) {

got_label =

;

*

= (*it)->GetVal();

*

+=

;

got_label =

;

*

+= (*it)->GetVal();

validation =

;

validation =

;

validation =

;

validation =

;

validation =

;

phenotype =

;

clinical_sig =

;

(clinical_sig.empty() && (*pnt_iter)->CanGetClinical_significance()) {

(phenotype.empty() && (*pnt_iter)->CanGetTerm()) {

phenotype = (*pnt_iter)->GetTerm();

sample_sex =

;

((*so_iter)->CanGetSource() &&

sample_sex = (*so_iter)->GetSource().GetName();

variant_type;

variant_type =

;

variant_type =

;

variant_type =

;

variant_type =

;

}

(var.

()) {

variant_type =

;

variant_type =

;

}

(var.

()) {

variant_type =

;

variant_type =

;

variant_type =

;

variant_type =

;

variant_type =

;

variant_type =

;

variant_type =

;

variant_type =

;

variant_type =

;

}

(var.

()) {

variant_type =

;

variant_type =

;

(child_num == 0) {

(child_num > 0) {

*

+=

;

*

+=

;

*

+= variant_type;

( !phenotype.empty() ) {

*

+=

+ phenotype;

( !clinical_sig.empty() ) {

*

+=

;

*

+= clinical_sig;

( !sample_sex.empty() ) {

*

+=

;

*

+= sample_sex;

*

+=

+ validation;

*

+=

;

*

+=

;

*

+=

;

*

+= variant_type;

( !phenotype.empty() ) {

*

+=

+ phenotype;

( !clinical_sig.empty() ) {

*

+=

;

*

+= clinical_sig;

( !sample_sex.empty() ) {

*

+=

;

*

+= sample_sex;

inh +=

;

inh +=

;

inh +=

;

inh +=

;

inh +=

;

inh +=

;

inh +=

;

*

+=

+ inh;

*

+=

+ validation;

allele_len = -1;

((*iter)->IsSetSeq() && (*iter)->GetSeq().IsLiteral()) {

allele_len = (*iter)->GetSeq().GetLiteral().GetLength();

(allele_len > -1) {

*

+=

;

*

+=

;

*

+=

;

CClone_ref::GetTypeInfo_enum_EPlacement_method();

( !method.empty() ) {

*

+=

+ method;

*

+=

;

*

+=

;

->GetLabel(&id_str);

end_map[seq.

()].push_back(id_str);

*

+=

+

*

+=

+

*

+=

+

*

+=

+ (*it)->GetQual() +

+ (*it)->GetVal();

*

+=

;

*

+=

+ (*it)->GetQual() +

+ (*it)->GetVal();

*

+=

;

(product_str != type_str) {

*

+=

+ (*it)->GetQual() +

+ (*it)->GetVal();

*

+=

;

(bf_interp.

()) {

(!Alleles.empty()) {

( !

->empty() ) {

*

+=

;

*

+=

;

( !qual.

().empty() ) {

pos = second_part.find(

);

(pos != string::npos)

second_part = second_part.substr(0, pos);

(!second_part.empty()) {

(!

.empty())

+= second_part;

(

.empty())

vector<string> quals{

,

,

,

,

,

,

,

,

,

,

,

,

};

(

&qual_name : quals) {

(

.empty())

vector<string> class_quals{

,

,

,

,

,

,

,

};

(

&qual_name : class_quals) {

&

= feat.GetNamedQual(qual_name);

(!

.empty())

(entry->

()) {

*

+=

;

*

+=

;

*

+=

;

*

+=

;

*

+=

;

*

+=

;

(asegs_type) {

*

+=

;

( !handle_set.

(sih).second ) {

( !

.empty() ) {

( handle_set.

() == 1 ){

*

+=

;

*

+=

;

*

+=

;

*

+=

;

( ; id_iter; ++id_iter) {

( !handle_set.

(sih).second ) {

( !

.empty() ) {

(handle_set.

() == 1) {

vector<bool> strands;

(;

< num_rows; ++

){

( !ids.empty() ) {

(

> num_rows_limit)

(

< num_rows) {

*

+=

;

(num_rows == 2 && strands.size() == 2) {

*

+=

;

*

+= strands[0] == strands[1] ?

:

;

*

+=

;

*

+=

;

coverage = 0.0;

*

+=

;

(coverage < 100.0 && coverage > 99.9) {

*

+=

;

sprintf(

,

, coverage);

(align_length < 1000000) {

identity = 0.0;

*

+=

;

identity = identities * 100.0 / align_length;

(identity < 100.0 && identity > 99.9) {

*

+=

;

sprintf(

,

, identity);

*

+=

;

*

+=

;

* id_trace = &id1;

+=

;

+=

;

+=

;

+=

;

+=

;

( !

.empty() ) {

& score = **iter;

score_str =

;

( !align )

;

*

+=

;

*

+=

;

*

+=

;

*

+=

;

(annot_data.

()) {

*

+=

;

*

+=

;

*

+=

;

*

+=

;

*

=

;

* title =

;

* name =

;

((*iter)->Which()) {

title = &(*iter)->GetTitle();

name = &(*iter)->GetName();

(annot_data.

()) {

=

;

items = annot_data.

().size();

* sid = annot_data.

().front()->GetLocation().GetId();

(

.empty()) {

}

(

!= s) {

(

.empty()) {

=

;

(

.empty()) {

=

;

items = annot_data.

().size();

items = annot_data.

().size();

items = annot_data.

().size();

=

;

items = annot_data.

().size();

*

=

;

( !extra.empty() ){

+=

+ extra +

;

*

+=

+ acc

*

+=

;

*

+=

;

*

+=

;

*

+=

;

char_count += idstr.length();

objects::CScope* scope)

*

+=

;

( !title.empty() ) {

( ; iter; ++iter) {

( !type_str.empty() && !content_str.empty() ) {

( !content_str.empty() ) {

*

+= content_str;

objects::CScope* scope)

*

=

;

*

+=

->CanGetTreetype() ?

->GetTreetype() :

;

*

+=

;

(

->IsSetLabel()) {

(

->IsSetTreetype()) {

*

+=

;

*

+=

;

*

+=

;

*

+=

;

(*iter)->GetGene().GetLabel(&s);

(*iter)->GetSource().GetOrg().GetLabel(&s);

*

+=

;

(iOtherIds != OtherIds.begin())

(*iOtherIds)->GetLabel(

);

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.

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.

@ eExtreme_Positional

numerical value

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.

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.

size_t GetSize(void) const

******************************************************************* Moved from plugins/algo/init ****...

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, objects::CScope *scope) const

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *) const

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *scope) const

const CBioseq & GetNucFromNucProtSet(void) const

const CBioseq & GetMasterFromSegSet(void) const

const CBioseq & GetGenomicFromGenProdSet(void) const

void GetLabel(string *label, ELabelType type) const

void GetLabel(string *label, ELabelType type, bool worst=false) const

void GetLabel(string *label) const

CRange< TSeqPos > GetSeqRange(TDim row) const

CDistanceMatrix label handler.

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType, objects::CScope *) const

CEntrezgene label handler.

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, objects::CScope *scope) const

CEntrezgene_Set label handler.

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, objects::CScope *scope) const

void GetLabel(const CObject &obj, string *str, CLabel::ELabelType type, objects::CScope *scope) const

bool IsSetDescr() const

retrieve the descriptor set for this project

const CProjectDescr & GetDescr() const

const CProjectFolder & GetData() const

retrieve our project's data, in the form of a project folder this may be a contrived entity,...

CGCAsssemblyHandler label handler.

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, objects::CScope *scope) const

string GetName() const

Retrieve the name of this assembly.

const CGC_AssemblyDesc & GetDesc() const

Retrieve the full set of assembly descriptors.

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

void GetLabel(string *label) const

void GetLabel(TGi gi, string *label) const

void AddCaches(const map< TGi, string > &caches)

map< TIntId, string > TGi2DescriptionMap

string GetLabel(TGi gi) const

bool HasLabel(TGi gi) const

CLabelDescriptionCacheImpl()

TGi2DescriptionMap m_DescrCache

void SetLabel(TGi gi, const string &label)

void GetLabel(string *label) const

void GetLabel(const CObject &obj, string *str, CLabel::ELabelType type, objects::CScope *scope) const

TSeqPos GetAlignLength(const CSeq_align &align, bool ungapped=false)

Compute the length of the alignment (= length of all segments, gaps + aligned)

int GetGapCount(const CSeq_align &align)

Compute the number of gaps in the alignment.

double GetPercentCoverage(CScope &scope, const CSeq_align &align, unsigned query=0)

Compute percent coverage of the query (sequence 0) (range 0-100)

int GetMismatchCount(CScope &scope, const CSeq_align &align)

Compute the number of mismatches in the alignment.

ESubtype GetSubtype(void) const

@ eSubtype_misc_structure

@ eSubtype_mobile_element

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *scope) const

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *) const

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

bool GetNamedScore(const string &id, int &score) const

Get score.

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *scope) const

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *scope) const

CUserFeatHandler m_UserHandler

bool x_UseCustomLabel(const objects::CSeq_feat &feat) const

void x_LabelFromQualifiers(const objects::CSeq_feat &feat, string &label) const

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *scope) const

void x_GetCustomLabel(const objects::CSeq_feat &feat, string &label) const

bool x_IncludeFeatureTypeInLabel(const objects::CSeq_feat &feat) const

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *scope) const

TSeqPos GetLength(void) const

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *scope) const

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Base class for all serializable objects.

CSnpBitfield is a facade for representing any version of the SNP bitfield.

bool IsTrue(EProperty prop) const

const char * GetVariationClassString() const

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *) const

Class designed to hold a set of tax-ids represented as (on) bits in a bit vector.

const TBitVec & GetSelectedTaxIds() const

Template class for iteration on objects of class C (non-medifiable version)

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

handler specific for User-object features

void GetLabel(const CObject &obj_in, string *label, CLabel::ELabelType type, CScope *scope) const

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *) const

SIZE_TYPE ErrorSize() const

SIZE_TYPE InfoSize() const

SIZE_TYPE CriticalSize() const

SIZE_TYPE WarningSize() const

SIZE_TYPE TotalSize() const

SIZE_TYPE FatalSize() const

CVariation label handler.

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, objects::CScope *scope) const

TValidated GetValidated(void) const

bool IsSetAllele_origin(void) const

TAllele_origin GetAllele_origin(void) const

bool IsUniparentalDisomy() const

bool IsDeletionInsertion() const

bool IsSetValidated(void) const

bool IsTranslocation() const

void GetLabel(const CObject &obj, string *label, CLabel::ELabelType type, CScope *scope) const

static TRsid GetRsid(const CMappedFeat &mapped_feat)

Return rsid of SNP.

static int GetLength(const CMappedFeat &)

Return distance of neighbors in flanking sequence.

vector< string > TAlleles

list of alleles belonging to particular SNP a deletion is represented by a "-"

static void GetAlleles(const CMappedFeat &mapped_feat, TAlleles &Alleles)

Return list of alleles encoded in qual.

static string ClinSigAsString(const CVariation_ref &var, ELetterCase LetterCase=eLetterCase_Mixed)

get a human-readable text for various clinical significance types

Constant iterator designed to enumerate "ON" bits.

enumerator first() const

Returns enumerator pointing on the first non-zero bit.

enumerator end() const

Returns enumerator pointing on the next bit after the last.

size_type count() const noexcept

population count (count of ON bits)

container_type::const_iterator const_iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

void(*)(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj) handler

API (CDeflineGenerator) for computing sequences' titles ("definitions").

SStaticPair< const char *, const char * > TPair

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 LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

const string & GetMsg(void) const

Get message string.

const string & FindName(TEnumValueType value, bool allowBadValue) const

Find name of the enum by its numeric value.

static string GetTypeIconAlias(const string &user_type, const string &user_subtype)

static void RegisterLabelHandler(const string &type, ILabelHandler &handler)

static const string sm_Tp_Sequence

static const string sm_Tp_ProjectItem

static void StopCache()

Stop cache instance (call once at gBench stop)

static const string sm_Tp_EntrezGeneRecord

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

static string FormatStringsOccurrences(const std::vector< string > &strings, const string &delimiter=", ")

static const string sm_Tp_Alignment

static const string sm_Tp_Annotation

static const string sm_Tp_Sequence_Set

static const string sm_SbTp_PhySet

static const string sm_SbTp_MutSet_Aln

static void AddCaches(const map< TGi, string > &caches)

static void GetIconAlias(const CObject &obj, string *alias, objects::CScope *scope=NULL)

static const string sm_SbTp_PhySet_Aln

static const string sm_SbTp_Undefined

static const string sm_SbTp_DNA

static const string sm_SbTp_EcoSet

static const string sm_Tp_TaxId_Set

static const string sm_SbTp_Graphs

static bool HasHandler(const CTypeInfo &type)

static const string sm_SbTp_NucProt

static void CacheSeqId(const objects::CSeq_id &id, objects::CScope *scope)

Generate and cache description label for the specified gi.

static string ConcatenateStrings(const std::vector< string > &strings, const string &delimiter=", ")

static void SetLabelByData(objects::CProjectItem &item, objects::CScope *scope=NULL)

static const string sm_Tp_Feature

static const string sm_SbTp_PopSet_Aln

static const string sm_SbTp_EcoSet_Aln

static const string sm_SbTp_GenProdSet

static const string sm_Tp_Alignment_Set

static const string sm_SbTp_Features

static const string sm_SbTp_Sequence_IDs

static void TruncateLabel(string *label, unsigned length_limit, unsigned length_tolerance)

truncate the label to some specific length with a desired leven of precision algorithm tries to analy...

static void InitCache()

Initialize cache instance (call once at gBench start)

static const string sm_SbTp_Table

static const string sm_Tp_ValidationResult

static const string sm_SbTp_Protein

static const string sm_SbTp_MutSet

static const string sm_SbTp_ProjectVer2

static const string sm_SbTp_SegSeq

static void RegisterTypeIcon(const string &user_type, const string &user_subtype, const string &icon_alias)

static const string sm_SbTp_Locations

static const string sm_SbTp_PopSet

static TLabelMap sm_LabelMap

static string GetTypeName()

static const string sm_Tp_Variation

void GetLabel(string &label, CLabel::ELabelType type) const

static const string sm_SbTp_Alignments

static TAliasMap sm_AliasMap

static const string sm_Tp_Sequence_ID

static const string sm_Tp_Location

static const string sm_Tp_Project

#define ENUM_METHOD_NAME(EnumName)

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

#define MSerial_AsnText

I/O stream manipulators –.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

CConstRef< CSeq_id > GetSeqIdOrNull(void) const

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

string GetLabel(const CSeq_id &id)

@ fLabel_Default

default options - always show the version

@ eContent

Untagged human-readable accession or the like.

@ eBoth

Type and content, delimited by a vertical bar.

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.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

TSeqPos GetStop(ESeqLocExtremes ext) const

@ eEmpty_Allow

ignore empty locations

ELabelType

For compatibility with legacy code.

@ fFGL_NoComments

Leave out comments, even as fallbacks.

@ fFGL_NoQualifiers

Leave out qualifiers.

@ fFGL_Content

Include its content if there is any.

@ fFGL_Type

Always include the feature's type.

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,...

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

bool IsOneBioseq(const CSeq_loc &loc, CScope *scope)

Returns true if all embedded CSeq_ids represent the same CBioseq, else false.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

@ eGetId_ForceGi

return only a gi-based seq-id

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &seqset, EMissing action=eMissing_Default)

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

CSeq_entry_Handle GetTopLevelEntry(void) const

Return a handle for the top-level seq-entry.

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

SAnnotSelector & SetLimitTSE(const CTSE_Handle &limit)

Limit annotations to those from the TSE only.

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

@ fWithCommas

Use commas as thousands separator.

const string & GetName(void) const

Get name of this type.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static const char label[]

const TOrg & GetOrg(void) const

Get the Org member data.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CEntrezgene > > Tdata

const TSource & GetSource(void) const

Get the Source member data.

const Tdata & Get(void) const

Get the member data.

const TGene & GetGene(void) const

Get the Gene member data.

bool IsSetLabel(void) const

user-defined label Check if a value has been assigned to Label data member.

const TTitle & GetTitle(void) const

Get the Title member data.

bool IsSetTitle(void) const

user-defined title for the workspace Check if a value has been assigned to Title data member.

const TLabel & GetLabel(void) const

Get the Label member data.

bool IsSetData(void) const

a set of extra analyses perfromed by the user each of these may have descriptors Check if a value has...

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetDesc(void) const

descriptive name Check if a value has been assigned to Desc data member.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

const TDb & GetDb(void) const

Get the Db member data.

TBool GetBool(void) const

Get the variant data.

bool IsSetClass(void) const

endeavor which designed this object Check if a value has been assigned to Class data member.

const TClass & GetClass(void) const

Get the Class member data.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

TId GetId(void) const

Get the variant data.

const TName & GetName(void) const

Get the Name member data.

const TLong_name & GetLong_name(void) const

Get the Long_name member data.

bool IsSetLong_name(void) const

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

bool IsSetName(void) const

Names of the assembly Check if a value has been assigned to Name data member.

bool IsSetId(void) const

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

const TDenseg & GetDenseg(void) const

Get the variant data.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

bool IsReal(void) const

Check if variant Real is selected.

E_Choice Which(void) const

Which variant is currently selected.

bool CanGetGenomic_id(void) const

Check if it is safe to call GetGenomic_id method.

vector< CRef< CScore > > TScore

E_Choice

Choice variants.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

vector< CRef< CSeq_id > > TIds

const TSpliced & GetSpliced(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

const TExons & GetExons(void) const

Get the Exons member data.

const TValue & GetValue(void) const

Get the Value member data.

bool CanGetProduct_id(void) const

Check if it is safe to call GetProduct_id method.

const TIds & GetIds(void) const

Get the Ids member data.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

list< CRef< CSeq_align > > Tdata

const TScore & GetScore(void) const

Get the Score member data.

TReal GetReal(void) const

Get the variant data.

const TDisc & GetDisc(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

@ e_not_set

No variant selected.

const TVal & GetVal(void) const

Get the Val member data.

TConcordant GetConcordant(void) const

Get the Concordant member data.

bool IsSetComment(void) const

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

const TClone & GetClone(void) const

Get the variant data.

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

bool IsUser(void) const

Check if variant User is selected.

bool IsSetUnique(void) const

OPTIONAL? Check if a value has been assigned to Unique data member.

const TRegion & GetRegion(void) const

Get the variant data.

const TTitle & GetTitle(void) const

Get the Title member data.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSetDescr(void) const

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

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetConcordant(void) const

OPTIONAL? Check if a value has been assigned to Concordant data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool CanGetSeq(void) const

Check if it is safe to call GetSeq method.

const TData & GetData(void) const

Get the Data member data.

list< CRef< CClone_seq > > Tdata

const TUser & GetUser(void) const

Get the variant data.

const TName & GetName(void) const

Get the Name member data.

TSupport GetSupport(void) const

Get the Support member data.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetPlacement_method(void) const

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

const TComment & GetComment(void) const

Get the Comment member data.

bool IsSetName(void) const

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

TUnique GetUnique(void) const

Get the Unique member data.

TSite GetSite(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TClone_seq & GetClone_seq(void) const

Get the Clone_seq member data.

TPlacement_method GetPlacement_method(void) const

Get the Placement_method member data.

const TSeq & GetSeq(void) const

Get the Seq member data.

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetProduct(void) const

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

const TVariation & GetVariation(void) const

Get the variant data.

bool IsRna(void) const

Check if variant Rna is selected.

bool CanGetSupport(void) const

Check if it is safe to call GetSupport method.

bool IsRegion(void) const

Check if variant Region is selected.

bool CanGetTitle(void) const

Check if it is safe to call GetTitle method.

const TImp & GetImp(void) const

Get the variant data.

bool IsSetClone_seq(void) const

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

bool CanGetComment(void) const

Check if it is safe to call GetComment method.

@ eSupport_supporting

sequence supports placement

@ eSupport_supports_other

supports a different placement

@ eSupport_prototype

sequence used to place clone

@ eSupport_non_supporting

does not support any placement

bool IsSetAccession(void) const

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

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

const TId & GetId(void) const

Get the Id member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

const TWhole & GetWhole(void) const

Get the variant data.

TFrom GetFrom(void) const

Get the From member data.

bool IsGeneral(void) const

Check if variant General is selected.

list< CRef< CSeq_loc > > Tdata

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

vector< TSeqPos > TPoints

const TLocal & GetLocal(void) const

Get the variant data.

bool IsSetStrand(void) const

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

bool IsLocal(void) const

Check if variant Local is selected.

const TPoints & GetPoints(void) const

Get the Points member data.

TStrand GetStrand(void) const

Get the Strand member data.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

TTo GetTo(void) const

Get the To 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.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_not_set

No variant selected.

const TSeq & GetSeq(void) const

Get the variant data.

TClass GetClass(void) const

Get the Class member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

@ eClass_equiv

a set of equivalent maps or seqs

@ eClass_parts

parts for 2 or 3

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_conset

constructed sequence + parts

@ eClass_wgs_set

whole genome shotgun project

@ eClass_mut_set

set of mutations

@ eClass_pir

converted pir

@ eClass_eco_set

ecological sample study

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gibb

geninfo backbone

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_pdb_entry

a complete PDB entry

@ eClass_genbank

converted genbank

@ eClass_swissprot

converted SWISSPROT

@ eClass_segset

segmented sequence + parts

@ eClass_pub_set

all the seqs from a single publication

const Tdata & Get(void) const

Get the member data.

const TGraph & GetGraph(void) const

Get the variant data.

const TLocs & GetLocs(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_align > > TAlign

const TIds & GetIds(void) const

Get the variant data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetDesc(void) const

used only for stand alone Seq-annots Check if a value has been assigned to Desc data member.

const TAlign & GetAlign(void) const

Get the variant data.

const TFtable & GetFtable(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CAnnotdesc > > Tdata

@ e_Ids

used for communication between tools

@ e_Locs

used for communication between tools

@ e_Name

a short name for this collection

@ e_Title

a title for this collection

bool CanGetAccession(void) const

Check if it is safe to call GetAccession method.

const TAccession & GetAccession(void) const

Get the Accession member data.

bool CanGetOther_ids(void) const

Check if it is safe to call GetOther_ids method.

bool CanGetId(void) const

Check if it is safe to call GetId method.

const TOther_ids & GetOther_ids(void) const

Get the Other_ids member data.

const TDescription & GetDescription(void) const

Get the Description member data.

bool CanGetDescription(void) const

Check if it is safe to call GetDescription method.

list< CRef< CDbtag > > TOther_ids

const TId & GetId(void) const

Get the Id member data.

const TInstance & GetInstance(void) const

Get the variant data.

const TVariant_prop & GetVariant_prop(void) const

Get the Variant_prop member data.

bool CanGetConsequence(void) const

Check if it is safe to call GetConsequence method.

bool CanGetMethod(void) const

Check if it is safe to call GetMethod method.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

bool IsSetVariant_prop(void) const

variant properties bit fields Check if a value has been assigned to Variant_prop data member.

list< CRef< CPhenotype > > TPhenotype

bool IsSetAllele_origin(void) const

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

const TId & GetId(void) const

Get the Id member data.

const TDelta & GetDelta(void) const

Get the Delta member data.

list< CRef< C_E_Somatic_origin > > TSomatic_origin

const TData & GetData(void) const

Get the Data member data.

const TPhenotype & GetPhenotype(void) const

Get the Phenotype member data.

bool CanGetSomatic_origin(void) const

Check if it is safe to call GetSomatic_origin method.

bool IsInstance(void) const

Check if variant Instance is selected.

TOther_validation GetOther_validation(void) const

Get the Other_validation member data.

list< CRef< C_E_Consequence > > TConsequence

const TSomatic_origin & GetSomatic_origin(void) const

Get the Somatic_origin member data.

const TConsequence & GetConsequence(void) const

Get the Consequence member data.

const TParent_id & GetParent_id(void) const

Get the Parent_id member data.

list< CRef< CDelta_item > > TDelta

bool IsSetOther_validation(void) const

has this variant been validated? While a boolean flag offers no subtle distinctions of validation met...

bool CanGetParent_id(void) const

Check if it is safe to call GetParent_id method.

bool IsSetId(void) const

ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP|rs12334',...

bool CanGetPhenotype(void) const

Check if it is safe to call GetPhenotype method.

bool CanGetId(void) const

Check if it is safe to call GetId method.

const TMethod & GetMethod(void) const

Get the Method member data.

TAllele_origin GetAllele_origin(void) const

Get the Allele_origin member data.

@ eMethod_E_optical_mapping

@ eAllele_origin_not_tested

@ eAllele_origin_paternal

@ eAllele_origin_tested_inconclusive

@ eAllele_origin_biparental

@ eAllele_origin_uniparental

@ eAllele_origin_maternal

@ eAllele_origin_inherited

@ eAllele_origin_other

stopper - 2^31

static void s_GetBioseq_setType(const CBioseq_set &bst, string *label)

static void s_GetAlignmentTooltip(const CSeq_align &align, string *label, CScope *scope)

static void s_BreakSeq_loc(const CSeq_loc &loc, vector< CRef< CSeq_loc > > &locs, CScope *scope)

static void s_GetDefline(const CSeq_id &id, CScope *scope, string *label)

static void s_GetCachedDescription(const CSeq_id &id, CScope *scope, string *label)

static CFastMutex s_DFLock

static void s_GetAnnotContent(const CSeq_annot &annot, string *label, CScope *scope)

DEFINE_STATIC_MUTEX(sm_Mutex)

static void s_GetSeq_TotalRangeLabel(const CSeq_loc &loc, string *label, CScope *scope, CLabel::ELabelType type)

static sequence::CDeflineGenerator s_DefGen

This class seems to be non-thread safe even as a stack var.

static bool s_IsCopyNumberMethod(const CVariation_ref::TMethod &method)

static const CSeq_id * s_GetLabel(const CSeq_loc &loc, string *label, CScope *scope, CLabel::ELabelType type, const CSeq_id *last_id=NULL)

static void s_GetBioseq_setContent(const CBioseq_set &bst, string *label, CScope *scope)

static void s_GetSeq_intervalLabel(const CSeq_interval &interval, string *label, CScope *scope, CLabel::ELabelType type, const CSeq_id *last_id=NULL)

static void s_GetGenProdContent(const CBioseq_set &bst, string *label, CScope *scope)

static void s_GetAlignmentContent(const CSeq_align &align, string *label, CScope *scope)

static void s_GetNucProtContent(const CBioseq_set &bst, string *label, CScope *scope)

static void s_GetIdLabel(const CBioseq_set &bst, string *label, CScope *scope)

static int s_GetChildNum(const objects::CSeq_feat &feat)

static void s_GetSeqLabel(const CSeq_id &id, string *label, CScope *scope, CLabel::ELabelType type)

static bool s_HasAlignment(const CBioseq_set &bst, CScope *scope)

static bool s_IsLOH(const CVariation_ref &var)

static SForceRegister sm_ForceRegistration

static std::unique_ptr< CLabelDescriptionCacheImpl > s_DescrCachePtr

static size_t s_CountSegments(const CSeq_align &align)

static void s_GetAlignmentType(const CSeq_align &align, string *label)

static void s_GetAnnotType(const CSeq_annot &annot, string *label)

static TGi s_GetGi(const CSeq_id &id, CScope *scope)

static void s_GetSegsetContent(const CBioseq_set &bst, string *label, CScope *scope)

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

Multi-threading – mutexes; rw-locks; semaphore.

Int4 delta(size_t dimension_, const Int4 *score_)

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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