NCBI C++ ToolKit
Macros | Functions
ftamain.cpp File Reference
#include <ncbi_pch.hpp>
#include "ftacpp.hpp"
#include <objects/seqset/Bioseq_set.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/submit/Submit_block.hpp>
#include <objects/biblio/Cit_sub.hpp>
#include <objects/biblio/Auth_list.hpp>
#include "index.h"
#include "sprot.h"
#include "embl.h"
#include "genbank.h"
#include <objtools/flatfile/ff2asn.h>
#include "ftanet.h"
#include <objtools/flatfile/flatfile_parser.hpp>
#include <objtools/flatfile/flatdefn.h>
#include "keyword_parse.hpp"
#include "flatfile_message_reporter.hpp"
#include "ftaerr.hpp"
#include <objtools/logging/listener.hpp>
#include "indx_blk.h"
#include "asci_blk.h"
#include "add.h"
#include "loadfeat.h"
#include "gb_ascii.h"
#include "sp_ascii.h"
#include "em_ascii.h"
#include "utilfeat.h"
#include "buf_data_loader.h"
#include "utilfun.h"
#include "entry.h"
+ Include dependency graph for ftamain.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.


#define THIS_FILE   "ftamain.cpp"


 USING_SCOPE (objects)
bool XMLAscii (ParserPtr pp)
void fta_init_gbdataloader ()
static void CkSegmentSet (ParserPtr pp)
static bool CompareAccs (const Indexblk *p1, const Indexblk *p2)
static bool CompareAccsV (const Indexblk *p1, const Indexblk *p2)
static bool CompareData (const Indexblk *p1, const Indexblk *p2)
static bool CompareDataV (const Indexblk *p1, const Indexblk *p2)
static void CheckDupEntries (ParserPtr pp)
static CRef< CSerialObjectMakeBioseqSet (ParserPtr pp)
static CRef< CSerialObjectMakeSeqSubmit (ParserPtr pp)
static void SetReleaseStr (ParserPtr pp)
static void GetAuthorsStr (ParserPtr pp)
static CRef< CSerialObjectCloseAll (ParserPtr pp)
static bool sParseFlatfile (CRef< CSerialObject > &ret, ParserPtr pp, bool already=false)
Int2 fta_main (ParserPtr pp, bool already)
static bool FillAccsBySource (Parser &pp, const string &source, bool all)
void Flat2AsnCheck (char *ffentry, char *source, char *format, bool accver, Parser::EMode mode, Int4 limit)
static void s_ReportFatalError (const string &msg, IObjtoolsListener *pListener)
TEntryListfta_parse_buf (Parser &pp, const char *buf)
bool fta_set_format_source (Parser &pp, const string &format, const string &source)
void fta_init_pp (Parser &pp)

Macro Definition Documentation


#define THIS_FILE   "ftamain.cpp"

Definition at line 76 of file ftamain.cpp.

Function Documentation

◆ CheckDupEntries()

static void CheckDupEntries ( ParserPtr  pp)

◆ CkSegmentSet()

static void CkSegmentSet ( ParserPtr  pp)

◆ CloseAll()

static CRef<CSerialObject> CloseAll ( ParserPtr  pp)

◆ CompareAccs()

static bool CompareAccs ( const Indexblk p1,
const Indexblk p2 

Definition at line 172 of file ftamain.cpp.

References Indexblk::acnum, and StringCmp().

Referenced by CheckDupEntries().

◆ CompareAccsV()

static bool CompareAccsV ( const Indexblk p1,
const Indexblk p2 

Definition at line 178 of file ftamain.cpp.

References Indexblk::acnum, i, StringCmp(), and Indexblk::vernum.

Referenced by CheckDupEntries().

◆ CompareData()

static bool CompareData ( const Indexblk p1,
const Indexblk p2 

◆ CompareDataV()

static bool CompareDataV ( const Indexblk p1,
const Indexblk p2 

◆ FillAccsBySource()

static bool FillAccsBySource ( Parser pp,
const string source,
bool  all 

◆ Flat2AsnCheck()

void Flat2AsnCheck ( char *  ffentry,
char *  source,
char *  format,
bool  accver,
Parser::EMode  mode,
Int4  limit 

◆ 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_pp()

void fta_init_pp ( Parser pp)

◆ fta_main()

Int2 fta_main ( ParserPtr  pp,
bool  already 

Definition at line 531 of file ftamain.cpp.

References sParseFlatfile().

Referenced by Flat2AsnCheck().

◆ fta_parse_buf()

TEntryList& fta_parse_buf ( Parser pp,
const char *  buf 

◆ fta_set_format_source()

bool fta_set_format_source ( Parser pp,
const string format,
const string source 

◆ GetAuthorsStr()

static void GetAuthorsStr ( ParserPtr  pp)

◆ MakeBioseqSet()

static CRef<CSerialObject> MakeBioseqSet ( ParserPtr  pp)

◆ MakeSeqSubmit()

static CRef<CSerialObject> MakeSeqSubmit ( ParserPtr  pp)

◆ s_ReportFatalError()

static void s_ReportFatalError ( const string msg,
IObjtoolsListener pListener 

Definition at line 731 of file ftamain.cpp.

References eDiag_Fatal, eUnknown, NCBI_THROW, and IObjtoolsListener::PutMessage().

Referenced by CFlatFileParser::Parse().

◆ SetReleaseStr()

static void SetReleaseStr ( ParserPtr  pp)

◆ sParseFlatfile()

static bool sParseFlatfile ( CRef< CSerialObject > &  ret,
ParserPtr  pp,
bool  already = false 


USING_SCOPE ( objects  )

◆ XMLAscii()

bool XMLAscii ( ParserPtr  pp)

Definition at line 1128 of file xm_ascii.cpp.

References Parser::accver, Indexblk::acnum, CScope::AddBioseq(), AssemblyGapsToDelta(), Indexblk::bases, BuildBioSegHeader(), CheckDupDates(), CheckFeatSeqLoc(), Parser::citat, Parser::cleanup, Parser::convert, CreateEntryBioseq(), Parser::curindx, Parser::DDBJ, DealWithGenes(), Parser::debug, Indexblk::division, Indexblk::drop, Parser::entries, EntryCheckDivCode(), Parser::entrylist, CSeq_inst_Base::eRepr_raw, ERR_DATE_IllegalDate, ERR_DIVISION_Mismatch, ERR_ENTRY_GBBlock_not_Empty, ERR_ENTRY_LongHTGSSequence, ERR_ENTRY_LongSequence, ERR_ENTRY_Parsed, ERR_ENTRY_ParsingComplete, ERR_ENTRY_Skipped, err_install(), ERR_QSCORE_FailedToParse, ERR_REFERENCE_No_references, ERR_SEGMENT_OnlyOneMember, ERR_SEGMENT_Rejected, ERR_SEQUENCE_BadData, ERR_TSA_UnexpectedPrimaryAccession, ErrPostEx, ErrPostStr, Parser::ff_get_qscore, Parser::ff_get_qscore_pp, FinalCleanup(), Parser::Flybase, Parser::format, fta_EntryCheckGBBlock(), fta_find_pub_explore(), fta_remove_cleanup_user_object(), fta_set_molinfo_completeness(), fta_set_strandedness(), fta_sort_descr(), fta_sort_seqfeat_cit(), fta_tsa_tls_comment_dblink_check(), FtaDeletePrefix(), Indexblk::gaps, GapsToDelta(), CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), GetDNAConv(), CBioseq_Base::GetInst(), GetProteinConv(), GetQSFromFile(), CSeq_inst_Base::GetRepr(), GetScope(), GetSeqExt(), Indexblk::htg, i, Parser::ign_bad_qs, Parser::indx, Indexblk::is_pat, Indexblk::is_prot, Indexblk::is_tls, Indexblk::is_tsa, Indexblk::is_wgs, CSeq_inst::IsNa(), CBioseq_Base::IsSetAnnot(), DataBlk::len, Parser::limit, LoadFeat(), Indexblk::locusname, MaybeCutGbblockSource(), MemFree(), DataBlk::mOffset, DataBlk::mpData, DataBlk::mpQscore, Parser::no_date, no_date(), no_reference(), CRef< C, Locker >::NotEmpty(), PackEntries(), PREFIX_ACCESSION, PREFIX_LOCUS, ProcessCitations(), ProcNucProt(), Indexblk::psip, Parser::qamode, QscoreToSeqAnnot(), Parser::qsfd, Indexblk::qslength, Parser::Refseq, CRef< C, Locker >::Reset(), CScope::ResetHistory(), Indexblk::segnum, Indexblk::segtotal, EntryBlk::seq_entry, SeqToDelta(), CBioseq_Base::SetId(), SEV_ERROR, SEV_INFO, SEV_REJECT, SEV_WARNING, Parser::source, StringEqu(), StringEquN(), StringLen(), StripSerialNumbers(), Indexblk::tsa_allowed, Parser::USPTO, GeneRefFeats::valid, Indexblk::vernum, Indexblk::xip, Parser::xml_comp, XMLCheckContigEverywhere(), XMLFakeBioSources(), XMLGetDescr(), XMLGetDivision(), XMLGetInst(), and XMLLoadEntry().

Referenced by fta_parse_buf(), and sParseFlatfile().

Modified on Tue May 28 05:52:49 2024 by rev. 669887