RetroSearch Browse

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Dbtag_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/general/Dbtag.cpp Source File

82 struct

STaxidTaxname {

84 const char

* m_species;

85 const char

* m_subspecies;

90

{ 7955, {

"Danio"

"rerio"

""

} },

91

{ 8022, {

"Oncorhynchus"

"mykiss"

""

} },

92

{ 9606, {

"Homo"

"sapiens"

""

} },

93

{ 9615, {

"Canis"

"lupus"

"familiaris"

} },

94

{ 9838, {

"Camelus"

"dromedarius"

""

} },

95

{ 9913, {

"Bos"

"taurus"

""

} },

96

{ 9986, {

"Oryctolagus"

"cuniculus"

""

} },

97

{ 10090, {

"Mus"

"musculus"

""

} },

98

{ 10093, {

"Mus"

"pahari"

""

} },

99

{ 10094, {

"Mus"

"saxicola"

""

} },

100

{ 10096, {

"Mus"

"spretus"

""

} },

101

{ 10098, {

"Mus"

"cookii"

""

} },

102

{ 10105, {

"Mus"

"minutoides"

""

} },

103

{ 10116, {

"Rattus"

"norvegicus"

""

} },

104

{ 10117, {

"Rattus"

"rattus"

""

} }

112 auto

it = _cont.find(_key);

113 if

(it == _cont.end())

116 if

(_key != it->first && _key != it->second.m_alias)

119 return

it->second.m_groups;

125 auto

it = _cont.find(_key);

126 if

(it == _cont.end())

129 if

(_key != it->first && _key != it->second.m_alias)

132

_retval = it->second.m_tag;

140 if

(

auto

it = _cont.find(v); it != _cont.end()) {

141 if

(it->second.m_alias == string_view(v))

142

correct_caps = it->second.m_alias;

144

correct_caps = it->first;

145 return

it->second.m_groups;

190 switch

(

id

.Which()) {

193 const string

& db =

GetDb

();

194 const string

str

id

.GetStr();

195 if

(

str

.size() > db.size() &&

str

[db.size()] ==

':' 220 const string

& db =

GetDb

();

232 bool

found = (group &

fSrc

);

250 const string

& db =

GetDb

();

274 const string

& db =

GetDb

();

276 auto

allowed = xFindStrict(db);

277 return

(allowed & group);

283 return

sc_SkippableDbXrefs.find(

GetDb

())

284

!= sc_SkippableDbXrefs.end();

296 const string

& db =

GetDb

();

298 if

(xGetStrict(db,

m_Type

))

307

correct_caps.clear();

313 const string

& db =

GetDb

();

317 auto

groups = xFindCorrectCaps(db, caps);

331

is_refseq = ((group &

fRefSeq

) != 0);

332

is_src = ((group &

fSrc

) != 0);

334 return

group !=

fNone

;

350 static

constexpr string_view

kFBan

"http://www.fruitfly.org/cgi-bin/annot/fban?"

;

351 static

constexpr string_view

kDictyPrim

"http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id="

;

352 static

constexpr string_view

kMiRBaseMat

"http://www.mirbase.org/cgi-bin/mature.pl?mature_acc="

;

353 static

constexpr string_view

kMaizeGDBInt

"https://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id="

;

354 static

constexpr string_view

kMaizeGDBStr

"https://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?term="

;

355 static

constexpr string_view

kHomdTax

"http://www.homd.org/taxon="

;

356 static

constexpr string_view

kHomdSeq

"http://www.homd.org/seq="

;

368

{

CDbtag::eDbtagType_ApiDB

"http://www.apidb.org/apidb/showRecord.do?name=GeneRecordClasses.ApiDBGeneRecordClass&primary_key="

383

{

CDbtag::eDbtagType_FBOL

"http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal%20barcodes&Fields=All&Rec="

386

{

CDbtag::eDbtagType_GABI

"https://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?Mode=ShowSequence&App=ncbi&SequenceId="

417

{

CDbtag::eDbtagType_OrthoMCL

"http://orthomcl.org/orthomcl/showRecord.do?name=GroupRecordClasses.GroupRecordClass&group_name="

423

{

CDbtag::eDbtagType_Phytozome

"https://phytozome.jgi.doe.gov/pz/portal.html#!results?search=0&crown=1&star=1&method=0&searchText="

516 auto

find_iter = sc_TaxIdTaxnameMap.find(taxid);

517 if

( find_iter == sc_TaxIdTaxnameMap.end() ) {

520 const

STaxidTaxname & taxinfo = find_iter->second;

521 return GetUrl

( taxinfo.m_genus, taxinfo.m_species, taxinfo.m_subspecies );

531 if

( taxname_arg.empty() || taxname_arg.length() > kMaxLen ) {

536 string

taxname = taxname_arg;

540 const char

ch = *str_iter;

551

vector<string> taxname_parts;

554 if

( taxname_parts.size() == 2 || taxname_parts.size() == 3 ) {

559

genus = taxname_parts[0];

560

species = taxname_parts[1];

562 if

( taxname_parts.size() == 3 ) {

563

subspecies = taxname_parts[2];

566 return GetUrl

( genus, species, subspecies );

574 const string

& species,

575 const string

& subspecies)

const 577 auto

it = sc_UrlMap.find(

GetType

());

578 if

(it == sc_UrlMap.end()) {

582 auto

prefix = it->second;

585 bool

nonInteger =

false

;

590

}

else if

(

GetTag

().IsId()) {

624

string::const_iterator tag_iter =

tag

.begin();

625 for

( ; tag_iter !=

tag

.end() && !

isdigit

(*tag_iter) ; ++tag_iter ) {

629 tag

tag

.substr(num_skip);

661 if

(

tag

[0] ==

'g'

) {

671 tag

"%20%5BUniSTS%20ID%5D"

;

690

}

else if

(

GetTag

().IsStr()) {

699 tag

tag

.substr(pos + 4);

701

}

else if

isdigit

((

unsigned char

)

tag

[0])) {

714 tag

.insert(0,

"id="

);

716 tag

.insert(0,

"name="

);

739

num_alpha == 3 && num_digit == 5 )

741

prefix =

"http://www.wormbase.org/search/protein/"

;

757 tag

"&decorator=influenza"

;

765 tag

"&decorator=vipr"

;

769 if

( ! genus.empty() ) {

770 string

taxname_url_piece = genus +

"+"

+ species;

771 if

( ! subspecies.empty() ) {

772

taxname_url_piece +=

"+"

+ subspecies;

776 "species=Homo+sapiens&"

777 "species="

+ taxname_url_piece +

"&"

) +

784

prefix =

"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=imgthla;id="

;

790

string::const_iterator tag_iter =

tag

.begin();

793 if

(*tag_iter ==

'P'

) {

795 if

(*tag_iter ==

'_'

) {

796

prefix =

"https://www.ncbi.nlm.nih.gov/protein/"

;

828 if

( ! genus.empty() && ! species.empty() ) {

834 string

spc = species;

837

abbrev =

gen

.substr(0, 1) + spc.substr(0, 1);

839 tag

"&db="

+ abbrev;

844 tag

"/#orthologs"

;

860 if

(

tag

.empty() )

return false

;

862 if

(

tag

.length() >= 16)

return false

;

870

string::const_iterator tag_iter =

tag

.begin();

874 for

( ; tag_iter !=

tag

.end() &&

isalpha

(*tag_iter); ++tag_iter ) {

877 for

( ; tag_iter !=

tag

.end() && *tag_iter ==

'_'

; ++tag_iter ) {

880 for

( ; tag_iter !=

tag

.end() &&

isdigit

(*tag_iter) ; ++tag_iter ) {

883 if

( tag_iter !=

tag

.end() && *tag_iter !=

' '

&& *tag_iter !=

'.'

) {

887 if

(numUndersc > 1)

return false

;

889

out_num_alpha = numAlpha;

890

out_num_digit = numDigits;

891

out_num_unscr = numUndersc;

893 if

(numUndersc == 0) {

894 if

(numAlpha == 1 && numDigits == 5)

return true

;

895 if

(numAlpha == 2 && numDigits == 6)

return true

;

896 if

(numAlpha == 3 && numDigits == 5)

return true

;

897 if

(numAlpha == 4 && numDigits == 8)

return true

;

898 if

(numAlpha == 4 && numDigits == 9)

return true

;

899 if

(numAlpha == 5 && numDigits == 7)

return true

;

900

}

else if

(numUndersc == 1) {

901 if

(numAlpha != 2 || (numDigits != 6 && numDigits != 8 && numDigits != 9))

return false

;

902 if

(

tag

[0] ==

'N'

tag

[0] ==

'X'

tag

[0] ==

'Z'

) {

903 if

(

tag

[1] ==

'M'

915 if

(

tag

[0] ==

'A'

tag

[0] ==

'Y'

) {

916 if

(

tag

[1] ==

'P'

)

return true

;

static constexpr string_view kDictyPrim

static constexpr string_view kHomdTax

static constexpr string_view kMaizeGDBInt

MAKE_CONST_SET(sc_SkippableDbXrefs, ct::tagStrNocase, { "BankIt", "NCBIFILE", "TMSMART" }) struct STaxidTaxname

static constexpr string_view kMaizeGDBStr

static constexpr auto sc_ApprovedTags

static constexpr string_view kHomdSeq

MAKE_CONST_MAP(sc_TaxIdTaxnameMap, TTaxId, STaxidTaxname, { { 7955, { "Danio", "rerio", "" } }, { 8022, { "Oncorhynchus", "mykiss", "" } }, { 9606, { "Homo", "sapiens", "" } }, { 9615, { "Canis", "lupus", "familiaris" } }, { 9838, { "Camelus", "dromedarius", "" } }, { 9913, { "Bos", "taurus", "" } }, { 9986, { "Oryctolagus", "cuniculus", "" } }, { 10090, { "Mus", "musculus", "" } }, { 10093, { "Mus", "pahari", "" } }, { 10094, { "Mus", "saxicola", "" } }, { 10096, { "Mus", "spretus", "" } }, { 10098, { "Mus", "cookii", "" } }, { 10105, { "Mus", "minutoides", "" } }, { 10116, { "Rattus", "norvegicus", "" } }, { 10117, { "Rattus", "rattus", "" } } }) namespace

static constexpr string_view kMiRBaseMat

static constexpr string_view kFBan

void GetLabel(string *label) const

EDbtagType GetType(void) const

static bool x_LooksLikeAccession(const string &tag, int &out_num_alpha, int &out_num_digit, int &out_num_unscr)

bool Match(const CDbtag &dbt2) const

const char * IsApprovedNoCase(EIsRefseq refseq=eIsRefseq_No, EIsSource is_source=eIsSource_No) const

string GetUrl(void) const

void InvalidateType(void)

bool SetAsMatchingTo(const CDbtag &dbt2)

int TDbtagGroup

holds bitwise OR of "EDbtagGroup"

@ eDbtagType_EnsemblGenomes_Gn

@ eDbtagType_EnsemblGenomes_Tr

@ eDbtagType_EnsemblRapid

@ eDbtagType_AceView_WormGenes

@ eDbtagType_UniProt_SwissProt

@ eDbtagType_PeptideAtlas

@ eDbtagType_RBGE_herbarium

@ eDbtagType_ApiDB_ToxoDB

@ eDbtagType_AllianceGenome

@ eDbtagType_PiroplasmaDB

@ eDbtagType_EnsemblGenomes

@ eDbtagType_UniProt_TrEMBL

@ eDbtagType_NCBIOrtholog

@ eDbtagType_ApiDB_CryptoDB

@ eDbtagType_MicrosporidiaDB

@ eDbtagType_ApiDB_PlasmoDB

bool GetDBFlags(bool &is_refseq, bool &is_src, string &correct_caps) const

bool IsApproved(EIsRefseq refseq=eIsRefseq_No, EIsSource is_source=eIsSource_No, EIsEstOrGss is_est_or_gss=eIsEstOrGss_No) const

int Compare(const CDbtag &dbt2) const

bool IsSkippable(void) const

int Compare(const CObject_id &oid2) const

static constexpr auto construct(init_type const(&init)[N])

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

static void DLIST_NAME() remove(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

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

Check if both objects contain the same values.

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,...

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

int Compare(const T &s1, const T &s2) const

Return difference between "s1" and "s2".

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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 SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

PNocase_Generic< string > PNocase

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 Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static string & ToLower(string &str)

Convert string to lower case â string& version.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ eNocase

Case insensitive compare.

static const char label[]

TTag & SetTag(void)

Assign a value to Tag data member.

const TTag & GetTag(void) const

Get the Tag member data.

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

const TDb & GetDb(void) const

Get the Db member data.

TDb & SetDb(void)

Assign a value to Db data member.

const TStr & GetStr(void) const

Get the variant data.

std::false_type tagStrNocase

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