NCBI C++ ToolKit
Classes | Macros | Functions | Variables
ftanet.cpp File Reference
#include <ncbi_pch.hpp>
#include "ftacpp.hpp"
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/taxon1/taxon1.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/biblio/Cit_gen.hpp>
#include <objects/biblio/Cit_art.hpp>
#include <objects/biblio/Cit_sub.hpp>
#include <objects/biblio/Cit_book.hpp>
#include <objects/biblio/Cit_let.hpp>
#include <objects/biblio/Cit_pat.hpp>
#include <objects/biblio/Cit_jour.hpp>
#include <objects/biblio/Auth_list.hpp>
#include <objects/biblio/Affil.hpp>
#include <objects/biblio/Author.hpp>
#include <objects/biblio/Imprint.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/pub/Pub_set.hpp>
#include <objects/biblio/ArticleIdSet.hpp>
#include <objects/biblio/ArticleId.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/edit/pub_fix.hpp>
#include <dbapi/driver/drivers.hpp>
#include "index.h"
#include <objtools/flatfile/flatdefn.h>
#include <objtools/flatfile/flatfile_parser.hpp>
#include <corelib/ncbi_message.hpp>
#include "ftaerr.hpp"
#include "asci_blk.h"
#include "ftamed.h"
#include "utilfun.h"
#include "ref.h"
#include "flatfile_message_reporter.hpp"
+ Include dependency graph for ftanet.cpp:

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Classes

struct  KwordBlk
 
class  CFindPub
 

Macros

#define THIS_FILE   "ftanet.cpp"
 
#define HEALTHY_ACC   "U12345"
 
#define TAX_SERVER_TIMEOUT   3
 

Functions

 USING_SCOPE (objects)
 
void fta_strip_pub_comment (string &comment, const KwordBlk *kbp)
 
static void fta_fix_last_initials (CName_std &namestd, bool initials)
 
static void fta_fix_affil (TPubList &pub_list, Parser::ESource source)
 
static void fta_fix_imprint_language (TPubList &pub_list)
 
static void fta_strip_er_remarks (CPubdesc &pub_descr)
 
static Uint1 fta_init_med_server (bool normalize)
 
static Uint1 fta_init_tax_server (void)
 
void fta_init_servers (ParserPtr pp)
 
void fta_fini_servers (ParserPtr pp)
 
void fta_fill_find_pub_option (ParserPtr pp, bool htag, bool rtag)
 
static void fta_check_pub_ids (TPubList &pub_list)
 
void fta_find_pub_explore (ParserPtr pp, TEntryList &seq_entries)
 
static void fix_synonyms (CTaxon1 &taxon, COrg_ref &org_ref)
 
static CRef< COrg_reffta_get_orgref_byid (ParserPtr pp, bool *drop, TTaxId taxid, bool isoh)
 
CRef< COrg_reffta_fix_orgref_byid (ParserPtr pp, TTaxId taxid, bool *drop, bool isoh)
 
static CRef< COrg_reffta_replace_org (ParserPtr pp, bool *drop, COrg_ref &org_ref, const Char *pn, int merge, Int4 attempt)
 
void fta_fix_orgref (ParserPtr pp, COrg_ref &org_ref, bool *drop, char *organelle)
 
static TGi fta_get_gi_for_seq_id (const CSeq_id &id)
 
Int4 fta_is_con_div (ParserPtr pp, const CSeq_id &id, const Char *acc)
 
void fta_init_gbdataloader ()
 

Variables

static const KwordBlk PubStatus []
 
static const STimeout s_timeout = { 3 , 0 }
 

Macro Definition Documentation

◆ HEALTHY_ACC

#define HEALTHY_ACC   "U12345"

Definition at line 86 of file ftanet.cpp.

◆ TAX_SERVER_TIMEOUT

#define TAX_SERVER_TIMEOUT   3

Definition at line 793 of file ftanet.cpp.

◆ THIS_FILE

#define THIS_FILE   "ftanet.cpp"

Definition at line 84 of file ftanet.cpp.

Function Documentation

◆ fix_synonyms()

static void fix_synonyms ( CTaxon1 taxon,
COrg_ref org_ref 
)
static

Definition at line 796 of file ftanet.cpp.

References COrg_ref_Base::SetSyn(), and CTaxon1::SetSynonyms().

Referenced by fta_get_orgref_byid().

◆ fta_check_pub_ids()

static void fta_check_pub_ids ( TPubList pub_list)
static

Definition at line 521 of file ftanet.cpp.

References ERR_REFERENCE_ArticleIdDiscarded, ErrPostEx, and SEV_ERROR.

Referenced by CFindPub::fix_pub_equiv().

◆ fta_fill_find_pub_option()

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

◆ fta_find_pub_explore()

void fta_find_pub_explore ( ParserPtr  pp,
TEntryList seq_entries 
)

◆ fta_fini_servers()

void fta_fini_servers ( ParserPtr  pp)

Definition at line 408 of file ftanet.cpp.

References GetPubmedClient(), and Parser::medserver.

◆ fta_fix_affil()

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

◆ fta_fix_imprint_language()

static void fta_fix_imprint_language ( TPubList pub_list)
static

◆ fta_fix_last_initials()

static void fta_fix_last_initials ( CName_std namestd,
bool  initials 
)
static

◆ fta_fix_orgref()

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

◆ fta_fix_orgref_byid()

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

◆ fta_get_gi_for_seq_id()

static TGi fta_get_gi_for_seq_id ( const CSeq_id id)
static

◆ fta_get_orgref_byid()

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

◆ fta_init_gbdataloader()

void fta_init_gbdataloader ( )

Definition at line 1071 of file ftanet.cpp.

References CObjectManager::GetInstance(), and CGBDataLoader::RegisterInObjectManager().

Referenced by sParseFlatfile().

◆ fta_init_med_server()

static Uint1 fta_init_med_server ( bool  normalize)
static

Definition at line 368 of file ftanet.cpp.

References GetPubmedClient(), Init(), and InitPubmedClient().

Referenced by fta_find_pub_explore(), and fta_init_servers().

◆ fta_init_servers()

void fta_init_servers ( ParserPtr  pp)

◆ fta_init_tax_server()

static Uint1 fta_init_tax_server ( void  )
static

Definition at line 377 of file ftanet.cpp.

References CTaxon1::Init().

Referenced by fta_fix_orgref(), fta_fix_orgref_byid(), and fta_init_servers().

◆ fta_is_con_div()

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

◆ fta_replace_org()

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

◆ fta_strip_er_remarks()

static void fta_strip_er_remarks ( CPubdesc pub_descr)
static

◆ fta_strip_pub_comment()

void fta_strip_pub_comment ( string comment,
const KwordBlk kbp 
)

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ PubStatus

const KwordBlk PubStatus[]
static
Initial value:
= {
{ "Publication Status: Available-Online prior to print", 51 },
{ "Publication Status : Available-Online prior to print", 52 },
{ "Publication_Status: Available-Online prior to print", 51 },
{ "Publication_Status : Available-Online prior to print", 52 },
{ "Publication-Status: Available-Online prior to print", 51 },
{ "Publication-Status : Available-Online prior to print", 52 },
{ "Publication Status: Online-Only", 31 },
{ "Publication Status : Online-Only", 32 },
{ "Publication_Status: Online-Only", 31 },
{ "Publication_Status : Online-Only", 32 },
{ "Publication-Status: Online-Only", 31 },
{ "Publication-Status : Online-Only", 32 },
{ "Publication Status: Available-Online", 36 },
{ "Publication Status : Available-Online", 37 },
{ "Publication_Status: Available-Online", 36 },
{ "Publication_Status : Available-Online", 37 },
{ "Publication-Status: Available-Online", 36 },
{ "Publication-Status : Available-Online", 37 },
{ nullptr, 0 }
}

Definition at line 96 of file ftanet.cpp.

Referenced by fta_strip_er_remarks().

◆ s_timeout

const STimeout s_timeout = { 3 , 0 }
static

Definition at line 794 of file ftanet.cpp.

Referenced by fta_get_orgref_byid(), and fta_replace_org().

Modified on Fri Jul 19 17:16:53 2024 by modify_doxy.py rev. 669887