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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/keywords__item_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/format/keywords_item.cpp Source File

*

[] = {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

(sc_STS_kw.find(keyword.c_str()) != sc_STS_kw.end()) {

(sc_GSS_kw.find(keyword.c_str()) != sc_GSS_kw.end()) {

(sc_EST_kw.find(keyword.c_str()) != sc_EST_kw.end()) {

(sc_GSS_kw.find(keyword.c_str()) != sc_GSS_kw.end()) {

(sc_EST_kw.find(keyword.c_str()) != sc_EST_kw.end()) {

(sc_STS_kw.find(keyword.c_str()) != sc_STS_kw.end()) {

(

.GetRepr() ) {

is_env_sample =

;

is_metagenome_source =

;

(! (*it)->IsSetSubtype())

;

is_env_sample =

;

(! (*it)->IsSetSubtype())

;

is_metagenome_source =

;

is_tsa =

;

(

.GetMolinfo()) {

(

.GetTech() ) {

(is_metagenome_source) {

( ! is_tsa &&

.IsProt() &&

.IsInNucProt() ) {

( parent_bioseq_set ) {

( ; desc_ci; ++desc_ci ) {

(errors.size() == 0) {

(

.IsEncode()) {

(

.IsGenomeAssembly() && !

.GetFinishingStatus().empty() ) {

(

.IsTPA() ) {

}

(

.IsRefSeq() ) {

(

.IsCrossKingdom() &&

.IsRSUniqueProt() ) {

list<string>* keywords =

;

(it->Which()) {

keywords = &(it->GetPir().GetKeywords());

keywords = &(it->GetGenbank().GetKeywords());

keywords = &(it->GetSp().GetKeywords());

keywords = &(it->GetEmbl().GetKeywords());

keywords = &(it->GetPrf().GetKeywords());

(list<string>, kwd, *keywords) {

(vector<string>, it, keywords) {

& kw = *k_itr;

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.

@ fUnreviewed_Unannotated

@ fUnverified_Contaminant

@ fUnverified_SequenceOrAnnotation

@ fUnverified_Misassembled

bool IsSetObject(void) const

void x_SetObject(const CSerialObject &obj)

void x_GatherInfo(CBioseqContext &ctx) override

EItem GetItemType() const override

void x_AddKeyword(const string &keyword)

void Format(IFormatter &formatter, IFlatTextOStream &text_os) const override

virtual void FormatKeywords(const CKeywordsItem &keys, IFlatTextOStream &text_os)=0

static bool is_valid(const char *num, int type, CONV_RESULT *cr)

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#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.

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

Case-insensitive equality of a substring with another string.

@ fSplit_Tokenize

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

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

bool IsSetOrg(void) const

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

list< CRef< CSubSource > > TSubtype

const TOrg & GetOrg(void) const

Get the Org member data.

@ eSubtype_environmental_sample

const TMod & GetMod(void) const

Get the Mod member data.

list< CRef< COrgMod > > TMod

bool IsSetOrgname(void) const

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

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSubtype_metagenome_source

const TSource & GetSource(void) const

Get the variant data.

TTech GetTech(void) const

Get the Tech member data.

bool CanGetTech(void) const

Check if it is safe to call GetTech method.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eRepr_map

ordered map of any kind

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_other

use Source.techexp

@ eTech_htc

high throughput cDNA

@ eTech_both

concept transl. w/ partial pept. seq.

@ eTech_targeted

targeted locus sets/studies

@ eTech_seq_pept_homol

sequenced peptide, ordered by homology

@ eTech_sts

Sequence Tagged Site.

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_seq_pept_overlap

sequenced peptide, ordered by overlap

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_concept_trans

conceptual translation

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_standard

standard sequencing

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_seq_pept

peptide was sequenced

@ eTech_survey

one-pass genomic sequence

@ eTech_htgs_0

single genomic reads for coordination

@ eTech_fli_cdna

full length insert cDNA

@ eTech_est

Expressed Sequence Tag.

@ eTech_concept_trans_a

conceptual transl. supplied by author

@ e_Embl

EMBL specific information.

@ e_User

user defined object

@ e_Pir

PIR specific info.

@ e_Genbank

GenBank specific info.

@ e_Prf

PRF specific information.

@ e_Sp

SWISSPROT specific info.

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

static const char *const sc_EST[]

static const char *const sc_STS[]

static bool s_CheckSpecialKeyword(const string &keyword, ETechFlags tech)

static bool x_OkayToAddKeyword(const string &keyword, vector< string > keywords)

static const char *const sc_GSS[]

CStaticArraySet< const char *, PCase_CStr > TStaticKeywordSet

DEFINE_STATIC_ARRAY_MAP(TStaticKeywordSet, sc_EST_kw, sc_EST)

Generic utility macros and templates for exploring NCBI objects.

#define FOR_EACH_STRING_IN_LIST(Itr, Var)

FOR_EACH_STRING_IN_LIST EDIT_EACH_STRING_IN_LIST.

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