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NCBI C++ ToolKit: src/objtools/flatfile/ftanet.cpp Source File

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, 51 },

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, 52 },

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(; kbp->

; kbp++) {

= p - comment.c_str();

j =

+ kbp->

;

(j < comment.size() && (comment[j] ==

|| comment[j] ==

))

comment.erase(

, j);

p = comment.empty() ?

: comment.c_str();

(

,

,

, p);

= strlen(

);

((*p ==

|| *p ==

) && !

(p + 1,

)) {

((*p ==

|| *p ==

) &&

(!

(p + 1,

) || !

(p + 1,

) ||

!

(p + 1,

) || !

(p + 1,

))) {

(!

(p + 1,

))

(!

(p + 1,

))

(!

(p + 1,

))

((*p ==

|| *p ==

) &&

!

(p + 1,

))) {

(!

(p + 1,

))

(!

(p + 1,

))

(

& pub : pub_list) {

(

& pub : pub_list) {

(pub->IsArticle()) {

}

(pub->IsSub()) {

}

(pub->IsGen()) {

(!

.IsSetAuthors() || !

.CanGetAuthors())

authors = &

.SetAuthors();

}

(pub->IsBook()) {

}

(pub->IsMan()) {

}

(pub->IsPatent()) {

(

& it :

) {

(it->IsSetAffil() && it->CanGetAffil() &&

& affil = it->SetAffil();

(it->IsSetName() && it->CanGetName() &&

it->GetName().IsName()) {

& namestd = it->SetName().SetName();

(

& pub : pub_list) {

(! pub->IsArticle())

language =

.GetImp().GetLanguage();

* lang = language.data();

(p = lang; *p !=

; p++)

(*p >=

&& *p <=

)

.SetImp().SetLanguage(lang);

(

& pub : pub_descr.

().

()) {

(! pub->IsArticle())

& art = pub->GetArticle();

status =

.GetImp().GetPubstatus();

(! comment.empty())

(! taxon_srv.

())

fta_init_pubseq(

)

* env_val = getenv(

);

idserver = env_val ? env_val :

;

env_val = getenv(

);

idusername = env_val ? env_val :

;

env_val = getenv(

);

idpassword = env_val ? env_val :

;

s_pubseq.reset(

CPubseqAccess(idserver.empty() ?

: idserver.c_str(),

idusername.empty() ?

: idusername.c_str(),

idpassword.empty() ?

: idpassword.c_str()));

(! s_pubseq || ! s_pubseq->CheckConnection())

fta_entrez_fetch_enable(

pp)

);

);

fta_entrez_fetch_disable(

pp)

findPubOptions.always_look,

findPubOptions.replace_cit,

findPubOptions.merge_ids,

(

& pub : pub_list) {

(pub->IsArticle()) {

(CPub_equiv::Tdata::iterator pub = pub_list.begin(); pub != pub_list.end();) {

(! (*pub)->IsMuid() && ! (*pub)->IsPmid()) {

,

(*pub)->IsMuid() ?

:

,

pub = pub_list.erase(pub);

list<CRef<CPub>> cit_arts;

(

& pPub : pub_equiv.

()) {

(! pPub->IsGen()) {

& cit_gen = pPub->SetGen();

(er || cit_gen.

().starts_with(

sv))) {

cit_arts.push_back(pPub);

(cit_arts.empty()) {

& cit_gen = cit_arts.front();

list<CRef<CPub>> others;

(

& pPub : pub_equiv.

()) {

(pPub->IsMuid() && ! pMuid)

(pPub->IsPmid() && ! pPmid)

(! pPub->IsArticle())

others.push_back(pPub);

(new_cit_art.

()) {

,

(

& pId : new_cit_art->

().

()) {

(pId->IsPubmed()) {

pmid = pId->GetPubmed();

}

(pId->IsMedline()) {

muid = pId->GetMedline();

);

}

(pmid != oldpmid) {

,

,

cit_arts.push_back(new_pub);

& pub_list = pub_equiv.

();

pub_list.push_back(pPmid);

pub_list.push_back(pMuid);

pub_list.splice(pub_list.end(), cit_arts);

if (pDesc->IsPub()) {

const auto& pubdesc = pDesc->GetPub();

return (pubdesc.IsSetComment() &&

fta_remark_is_er(pubdesc.GetComment()));

(

& pDescr : descrs.Set()) {

(! pDescr->IsPub())

fix_pub_equiv(pub_descr.

(), er);

(m_pParser->qamode)

(

& pAnnot : annots) {

(! pAnnot->IsSetData() || ! pAnnot->GetData().IsFtable())

(

& pFeat : pAnnot->SetData().SetFtable()) {

(pFeat->IsSetData() && pFeat->GetData().IsPub())

fix_pub_equiv(pub_descr.

(), er);

(m_pParser->qamode)

(! pFeat->IsSetCit()) {

(

& pPub : pFeat->SetCit().SetPub()) {

fix_pub_annot(*pPub, er);

(

& pEntry : seq_entries) {

(bio_set->SetAnnot(), bio_set->SetDescr());

(bio_set->GetDescr().Get().empty())

bio_set->ResetDescr();

(bio_set->SetAnnot().empty())

bio_set->ResetAnnot();

(bioseq->SetAnnot(), bioseq->SetDescr());

(bioseq->GetDescr().Get().empty())

bioseq->ResetDescr();

(bioseq->SetAnnot().empty())

bioseq->ResetAnnot();

find_pub.

(seq_entries);

(

& org_syn : org_ref.

()) {

(

& tax_syn : tax_org_ref.

()) {

(org_syn == tax_syn) {

,

org_ref.

().clear();

connection_failed =

;

(

= 0;

< 3 && taxdata.

(); ++

) {

taxdata = taxon.

(taxid);

connection_failed =

;

(taxdata.

()) {

(connection_failed) {

(taxdata->GetIs_species_level() != 1 && ! isoh) {

ret->

(taxdata->GetOrg());

(taxid <= ZERO_TAX_ID && pp->taxserver == 0)

connection_failed =

;

(

= 0;

< 3 && taxdata.

(); ++

) {

taxdata = taxon.

(org_ref);

connection_failed =

;

(taxdata.

()) {

(connection_failed) {

(taxdata->GetIs_species_level() != 1 && (ibp->

==

||

ret->

(taxdata->GetOrg());

last_char = taxname.size();

(; last_char; --last_char) {

(!

(taxname[last_char]))

(!

(taxname[last_char]))

org_ref.

(taxname.substr(0, last_char));

organelle_str(organelle),

space(taxname.size() ?

:

);

old_taxname = taxname;

taxname = organelle_str + space + taxname;

(new_org_ref.

() && attempt == 1) {

org_ref.

(*new_org_ref);

(;

< 5;

++) {

CPubseqAccess::IdGiClass id_gi;

CPubseqAccess::IdBlobClass id_blob;

(! s_pubseq->GetIdGiClass(gi, id_gi) || ! s_pubseq->GetIdBlobClass(id_gi, id_blob) ||

id_blob.div[0] ==

) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void ShrinkSpaces(char *line)

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

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

void Apply(TEntryList &entries)

list< CRef< CSeq_entry > > TEntryList

unique_ptr< edit::CPubFix > m_pPubFix

void find_pub(list< CRef< CSeq_annot >> &annots, CSeq_descr &descrs)

void fix_pub_annot(CPub &pub, bool er)

void fix_pub_equiv(CPub_equiv &pub_equiv, bool er)

unique_ptr< CPubFixMessageListener > m_pPubFixListener

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

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

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

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

CRef< CTaxon2_data > GetById(TTaxId tax_id)

TTaxId GetTaxIdByOrgRef(const COrg_ref &inp_orgRef)

CConstRef< CTaxon2_data > LookupMerge(COrg_ref &inp_orgRef, string *psLog=0, TOrgRefStatus *pStatusOut=0)

bool SetSynonyms(bool on_off)

CRef< CTaxon2_data > Lookup(const COrg_ref &inp_orgRef, string *psLog=0)

Template class for iteration on objects of class C.

#define ERR_REFERENCE_UnusualPubStatus

#define ERR_SERVER_NotUsed

#define ERR_SERVER_NoTaxLookup

#define ERR_SERVER_Failed

#define ERR_REFERENCE_ArticleIdDiscarded

#define ERR_REFERENCE_MuidPmidMissMatch

#define ERR_ORGANISM_TaxIdNotSpecLevel

#define ERR_ACCESSION_CannotGetDivForSecondary

#define ERR_SERVER_NoPubMedLookup

#define ERR_ORGANISM_TaxNameNotFound

#define ERR_REFERENCE_InvalidPmid

#define ERR_SERVER_TaxServerDown

#define ERR_ORGANISM_TaxIdNotUnique

#define ERR_SERVER_TaxNameWasFound

#define ERR_REFERENCE_CitArtLacksPmid

#define ERR_ORGANISM_NewSynonym

#define ERR_REFERENCE_DifferentPmids

list< CRef< objects::CSeq_entry > > TEntryList

std::list< CRef< objects::CPub > > TPubList

#define FtaErrPost(sev, level,...)

edit::CEUtilsUpdater * GetPubmedClient()

void InitPubmedClient(bool normalize)

CRef< CCit_art > FetchPubPmId(TEntrezId pmid)

static CRef< COrg_ref > fta_get_orgref_byid(ParserPtr pp, bool *drop, TTaxId taxid, bool isoh)

Int4 fta_is_con_div(ParserPtr pp, const CSeq_id &id, const Char *acc)

#define TAX_SERVER_TIMEOUT

void fta_find_pub_explore(ParserPtr pp, TEntryList &seq_entries)

static void fta_check_pub_ids(TPubList &pub_list)

static TGi fta_get_gi_for_seq_id(const CSeq_id &id)

void fta_fini_servers(ParserPtr pp)

CRef< COrg_ref > fta_fix_orgref_byid(ParserPtr pp, TTaxId taxid, bool *drop, bool isoh)

void fta_init_servers(ParserPtr pp)

static void fta_fix_affil(TPubList &pub_list, Parser::ESource source)

static void fta_fix_last_initials(CName_std &namestd, bool initials)

static Uint1 fta_init_tax_server(void)

void fta_init_gbdataloader()

static const STimeout s_timeout

void fta_fill_find_pub_option(ParserPtr pp, bool htag, bool rtag)

static CRef< COrg_ref > fta_replace_org(ParserPtr pp, bool *drop, COrg_ref &org_ref, const Char *pn, int merge, Int4 attempt)

static void fta_fix_imprint_language(TPubList &pub_list)

static void fix_synonyms(CTaxon1 &taxon, COrg_ref &org_ref)

static const KwordBlk PubStatus[]

void fta_strip_pub_comment(string &comment, const KwordBlk *kbp)

static void fta_strip_er_remarks(CPubdesc &pub_descr)

static Uint1 fta_init_med_server(bool normalize)

void fta_fix_orgref(ParserPtr pp, COrg_ref &org_ref, bool *drop, char *organelle)

static const struct name_t names[]

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

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

#define ENTREZ_ID_TO(T, entrez_id)

#define TAX_ID_TO(T, tax_id)

SStrictId_Tax::TId TTaxId

Taxon id type.

void DBAPI_RegisterDriver_FTDS(void)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

TGi GetGiForId(const objects::CSeq_id &id, CScope &scope, EGetIdType flags=0)

Given a Seq-id retrieve the corresponding GI.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

bool Empty(void) const THROWS_NONE

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

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

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

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

char Char

Alias for char.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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.

@ eNocase

Case insensitive compare.

bool CanGetAffil(void) const

Check if it is safe to call GetAffil method.

bool IsSetAffil(void) const

author affiliation Check if a value has been assigned to Affil data member.

bool IsSetAuthors(void) const

authors (ANSI requires) Check if a value has been assigned to Authors data member.

const TJournal & GetJournal(void) const

Get the variant data.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

const TFrom & GetFrom(void) const

Get the From member data.

const TCit & GetCit(void) const

Get the Cit member data.

const TAffil & GetAffil(void) const

Get the Affil member data.

void SetFrom(TFrom &value)

Assign a value to From data member.

void SetAffil(TAffil &value)

Assign a value to Affil data member.

bool IsSetFrom(void) const

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

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

bool IsSetAuthors(void) const

not necessarily authors of the paper Check if a value has been assigned to Authors data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

bool IsSetCit(void) const

anything, not parsable Check if a value has been assigned to Cit data member.

list< CRef< CAuthor > > TStd

const Tdata & Get(void) const

Get the member data.

TStr & SetStr(void)

Select the variant.

bool CanGetAuthors(void) const

Check if it is safe to call GetAuthors method.

void SetCit(TCit &value)

Assign a value to Cit data member.

bool IsSetNames(void) const

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

bool CanGetCit(void) const

Check if it is safe to call GetCit method.

bool IsSetAuthors(void) const

author/inventor Check if a value has been assigned to Authors data member.

E_Choice Which(void) const

Which variant is currently selected.

void SetNames(TNames &value)

Assign a value to Names data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

bool CanGetNames(void) const

Check if it is safe to call GetNames method.

bool CanGetAuthors(void) const

Check if it is safe to call GetAuthors method.

bool IsSetIds(void) const

lots of ids Check if a value has been assigned to Ids data member.

bool IsSetAuthors(void) const

authors Check if a value has been assigned to Authors data member.

bool IsJournal(void) const

Check if variant Journal is selected.

const TNames & GetNames(void) const

Get the Names member data.

bool IsSetCit(void) const

same fields as a book Check if a value has been assigned to Cit data member.

const TIds & GetIds(void) const

Get the Ids member data.

bool CanGetAuthors(void) const

Check if it is safe to call GetAuthors method.

bool CanGetAuthors(void) const

Check if it is safe to call GetAuthors method.

E_Choice Which(void) const

Which variant is currently selected.

@ ePubStatus_ppublish

published in print by publisher

@ ePubStatus_aheadofprint

epublish, but will be followed by print

@ ePubStatus_epublish

published electronically by publisher

void SetInitials(const TInitials &value)

Assign a value to Initials data member.

bool IsSetSuffix(void) const

Jr, Sr, III Check if a value has been assigned to Suffix data member.

void SetLast(const TLast &value)

Assign a value to Last data member.

bool IsSetInitials(void) const

first + middle initials Check if a value has been assigned to Initials data member.

bool IsSetLast(void) const

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

void SetSuffix(const TSuffix &value)

Assign a value to Suffix data member.

bool CanGetSyn(void) const

Check if it is safe to call GetSyn method.

void ResetSyn(void)

Reset Syn data member.

TSyn & SetSyn(void)

Assign a value to Syn data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TSyn & GetSyn(void) const

Get the Syn member data.

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

bool IsSetTaxname(void) const

preferred formal name Check if a value has been assigned to Taxname data member.

bool IsSetSyn(void) const

synonyms for taxname or common Check if a value has been assigned to Syn data member.

TPmid & SetPmid(void)

Select the variant.

TMuid & SetMuid(void)

Select the variant.

const TPmid & GetPmid(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

const Tdata & Get(void) const

Get the member data.

TEquiv & SetEquiv(void)

Select the variant.

bool IsEquiv(void) const

Check if variant Equiv is selected.

TMuid GetMuid(void) const

Get the variant data.

TArticle & SetArticle(void)

Select the variant.

void SetAccession(const TAccession &value)

Assign a value to Accession data member.

TGenbank & SetGenbank(void)

Select the variant.

bool IsSetComment(void) const

any comment on this pub in context Check if a value has been assigned to Comment data member.

void ResetComment(void)

Reset Comment data member.

void SetPub(TPub &value)

Assign a value to Pub data member.

const TComment & GetComment(void) const

Get the Comment member data.

const Tdata & Get(void) const

Get the member data.

void SetComment(const TComment &value)

Assign a value to Comment data member.

const TPub & GetPub(void) const

Get the Pub member data.

const CharType(& source)[N]

int strcmp(const char *str1, const char *str2)

IMessage/IMessageListener interfaces and basic implementations.

void SleepSec(unsigned long sec, EInterruptOnSignal onsignal=eRestartOnSignal)

Sleep.

User-defined methods of the data storage class.

CRef< CPub > journal(ParserPtr pp, char *bptr, char *eptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, bool has_muid, CRef< CCit_art > &cit_art, Int4 er)

vector< IndexblkPtr > entrylist

Char * StringIStr(const Char *where, const Char *what)

static wxAcceleratorEntry entries[3]

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