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

=

;

& tax_id_file,

is_na = bsh.

();

genome_specific_search =

;

( !tax_id_file.empty() ) {

(tax_id == NStr::StringToNumeric<TTaxId>(line)) {

genome_specific_search =

;

source_id_str;

entrezdb_tag =

;

entrezdb_tag =

;

entrezdb_tag =

;

entrezdb_tag =

;

pair<string, string>

;

(

,

),

(

,

),

=

;

(

= 0;

<

; ++

) {

= source_id_str;

url = entrezdb_tag + source_id_str +

+

;

= source_id_str;

params(

+ source_id_str);

params +=

;

params +=

;

extra_params(

);

url =

+ params + extra_params;

(genome_specific_search) {

params +=

;

name =

;

url =

;

& tax_id_file,

exclude_self_links)

( !loc_obj.

() ) {

loc.

(&loc_obj);

& tax_id_file,

exclude_self_links)

is_na = bsh.

();

genome_specific_search =

;

( !tax_id_file.empty() ) {

(tax_id == NStr::StringToNumeric<TTaxId>(line)) {

genome_specific_search =

;

source_id_str;

entrezdb_tag =

;

entrezdb_tag =

;

entrezdb_tag =

;

entrezdb_tag =

;

product_id_str;

is_product_na =

;

is_product_na = bsh.

();

=

;

pair<string, string>

;

(

,

),

(

,

),

(!exclude_self_links) {

(

= 0;

<

; ++

) {

= source_id_str + range_str;

url = entrezdb_tag + source_id_str +

+

+

= source_id_str + range_str;

url =

;

params(

+ source_id_str);

extra_params(

);

params +=

;

params +=

;

url = url + params + extra_params;

(genome_specific_search) {

params +=

;

name =

;

= source_id_str + range_str;

url =

;

product_db =

;

product_db =

;

pair<string, string>

;

(

,

),

(

,

),

(

,

)

(

= 0;

<

; ++

) {

( !is_product_na ) {

url = product_db + product_id_str +

+

;

params(

+ product_id_str);

extra_params(

);

extra_params +=

extra_params +=

url =

+ params + extra_params;

(links,

, name, product_id_str, url, relative);

(genome_specific_search) {

(!is_product_na) {

params +=

;

name =

;

url =

;

(links,

, name, product_id_str, url, relative);

( (*iter)->GetType().IsStr() &&

((*link_iter)->GetData().IsStr()) {

url = (*link_iter)->GetData().GetStr();

( !url.empty() && (*link_iter)->GetLabel().IsStr()) {

= (*link_iter)->GetLabel().GetStr();

pos =

.find_first_of(

);

(pos != string::npos) {

( !

.empty() ) {

url =

+

;

((*iter)->GetType().IsStr() &&

!(*iter)->GetData().empty()) {

name =

;

((*iter)->GetType().GetStr() ==

) {

(fields.size() < 5) {

= (*f_iter)->GetLabel().GetStr();

url =

+ (*f_iter)->GetData().GetStr();

url =

+ term;

}

((*iter)->GetType().GetStr() ==

) {

((*f_iter)->GetLabel().IsStr() && (*f_iter)->GetData().IsStr()) {

= (*f_iter)->GetLabel().GetStr();

term = (*f_iter)->GetData().GetStr();

( !term.empty() ) {

url =

+ term;

product_id_str;

is_product_na =

;

is_product_na = bsh.

();

=

;

name =

;

params(

+ product_id_str);

extra_params(

);

extra_params +=

extra_params +=

url =

+ params + extra_params;

(links,

, name, product_id_str, url, relative);

add_parent_gene_dbxrefs,

(!loc_obj.

()) {

loc.

(&loc_obj);

add_parent_gene_dbxrefs,

=

;

name =

;

=

+ rsid;

url =

+ rsid;

name =

;

url =

+ rsid +

;

name =

;

url =

+ rsid;

name =

;

url =

+ rsid;

( ; feat_iter; ++feat_iter) {

( !sGeneLocus.empty() ) {

name =

;

+=

+ sGeneLocus +

;

url =

+ rsid +

+ sGeneLocus;

&

,

& name,

&

,

& url,

edited_url(url);

((links[

])[name]).push_back(std::pair<string, string>(

, edited_url));

add_parent_gene_dbxrefs,

=

;

((*iter)->GetType()) {

(*iter)->GetLabel(&label_str);

pos = label_str.find(

);

pos = label_str.rfind(

);

name = label_str.substr(0, pos);

= label_str.substr(pos + 1);

url = tax_id !=

? (*iter)->GetUrl(tax_id) : (*iter)->GetUrl();

(

.empty() || url.empty()) {

gene_symbol_feat =

;

(gene_symbol_feat.

()) {

gene_id = (*iter)->GetTag().GetId();

feat_iter->GetNamedDbxref(

);

(

&&

->GetTag().GetId() == gene_id) {

gene_symbol_feat = feat_iter->GetSeq_feat();

(gene_symbol_feat.

()) {

(!gene_symbol.empty()) {

+=

+ gene_symbol +

;

User-defined methods of the data storage class.

static void AddDbxrefFeatureLinks(const objects::CSeq_feat &feat, const objects::CBioseq_Handle &handle, TLinksMap &links, bool add_parent_gene_dbxrefs=true, bool relative=true)

static void AddSequenceLinks(const objects::CSeq_id_Handle &idh, const string &tax_id_file, objects::CScope &scope, TLinksMap &links, TSeqPos from=0, TSeqPos to=0, bool relative=true)

static void AddDbxrefLinksForSNP(const objects::CSeq_feat &feat, const CRef< objects::CDbtag > &dbt, objects::CScope &scope, TLinksMap &links, bool relative=true)

static void AddBlastProductLink(const objects::CSeq_feat &feat, objects::CScope &scope, TLinksMap &links, bool relative)

static void AddFeatureLinks(const objects::CSeq_feat &feat, const objects::CBioseq_Handle &handle, const string &tax_id_file, TLinksMap &links, bool relative=true, bool exclude_self_links=false)

static void x_AddLink(TLinksMap &links, const string &type, const string &name, const string &label, const string &url, bool relative=true)

static void x_AddDbxrefFeatureLinks(const objects::CSeq_feat &feat, const objects::CSeq_loc &loc, objects::CScope &scope, objects::CBioseq_Handle &bsh, TTaxId tax_id, TLinksMap &links, bool add_parent_gene_dbxrefs=true, bool relative=true)

ESubtype GetSubtype(void) const

namespace ncbi::objects::

CConstRef< CDbtag > GetNamedDbxref(const CTempString &db) const

Return a specified DB xref.

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

bool IsTrue(EProperty prop) const

@ eHasSnp3D

Has 3D structure SNP3D.

static TRsid GetRsid(const CMappedFeat &mapped_feat)

Return rsid of SNP.

static const TPair sc_Pairs[]

SStaticPair< const char *, const char * > TPair

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

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

static CRef< objects::CSeq_loc > MixLocToLoc(const objects::CSeq_loc &mix_loc, const objects::CBioseq_Handle &handle)

Create a new seq-loc with a unique seq-id from a "mixed" loc.

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

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...

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

CSeq_id::E_Choice Which(void) const

string GetLabel(const CSeq_id &id)

TRange GetTotalRange(void) const

const CSeq_id * GetId(void) const

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

CMappedFeat GetBestGeneForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

@ fFGL_Content

Include its content if there is any.

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,...

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

@ eGetId_Best

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

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

TObjectType & GetObject(void) const

Get object.

position_type GetLength(void) const

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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

Convert int to string.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

const TLocus & GetLocus(void) const

Get the Locus member 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 TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

vector< CRef< CUser_field > > TData

TId GetId(void) const

Get the variant data.

vector< CRef< CDbtag > > TDbxref

E_Choice Which(void) const

Which variant is currently selected.

const TExts & GetExts(void) const

Get the Exts member data.

list< CRef< CUser_object > > TExts

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetExts(void) const

set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.

const TGene & GetGene(void) const

Get the variant data.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

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 IsLocal(void) const

Check if variant Local is selected.

bool IsWhole(void) const

Check if variant Whole is selected.

@ eNa_strand_both

in forward orientation

const TSample_id & GetSample_id(void) const

Get the Sample_id member data.

const TId & GetId(void) const

Get the Id member data.

const TParent_id & GetParent_id(void) const

Get the Parent_id member data.

bool CanGetParent_id(void) const

Check if it is safe to call GetParent_id method.

bool CanGetSample_id(void) const

Check if it is safe to call GetSample_id method.

bool CanGetId(void) const

Check if it is safe to call GetId method.

static const string kCommonUrl

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

std::istream & in(std::istream &in_, double &x_)

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

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