buf_data_loader.cpp File Reference

#include <ncbi_pch.hpp>
#include "ftacpp.hpp"
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqcode/Seq_code_type.hpp>
#include "index.h"
#include "embl.h"
#include "sprot.h"
#include "genbank.h"
#include <objtools/flatfile/flatfile_parse_info.hpp>
#include <objtools/flatfile/flatfile_parser.hpp>
#include <objtools/flatfile/flat2err.h>
#include "utilfun.h"
#include "ftaerr.hpp"
#include "ftablock.h"
#include "gb_ascii.h"
#include "asci_blk.h"
#include "buf_data_loader.h"

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Macros
#define	THIS_FILE   "buf_data_loader.cpp"

Functions
static char *	get_sequence_text (ParserPtr parser, const string &accession, int version)
static bool	get_accession_from_id (const CSeq_id &id, string &accession, int &version)
static int	add_entry (ParserPtr pp, const char *acc, Int2 vernum, DataBlkPtr entry)
static void	AddToIndexBlk (DataBlkPtr entry, IndexblkPtr ibp, Parser::EFormat format)
CRef< CBioseq >	get_bioseq (ParserPtr pp, DataBlkPtr entry, const CSeq_id &id)
static DataBlkPtr	make_entry (char *entry_str)
static CRef< CBioseq >	parse_entry (ParserPtr pp, char *entry_str, const string &accession, int ver, const CSeq_id &id)
size_t	CheckOutsideEntry (ParserPtr pp, const char *acc, Int2 vernum)

Macro Definition Documentation

THIS_FILE

#define THIS_FILE   "buf_data_loader.cpp"

Definition at line 63 of file buf_data_loader.cpp.

Function Documentation

add_entry()

static int add_entry ( ParserPtr  pp, const char *  acc, Int2  vernum, DataBlkPtr  entry  )

static

Definition at line 165 of file buf_data_loader.cpp.

References Parser::accver, Indexblk::acnum, LocusCont::bases, LocusCont::bp, LocusCont::date, LocusCont::div, Parser::entrylist, Parser::format, Parser::GenBank, i, Parser::indx, Indexblk::lc, DataBlk::len, DataBlk::mOffset, LocusCont::molecule, ParFlat_COL_BASES, ParFlat_COL_BASES_NEW, ParFlat_COL_BP, ParFlat_COL_BP_NEW, ParFlat_COL_DATE, ParFlat_COL_DATE_NEW, ParFlat_COL_DIV, ParFlat_COL_DIV_NEW, ParFlat_COL_MOLECULE, ParFlat_COL_MOLECULE_NEW, ParFlat_COL_STRAND, ParFlat_COL_STRAND_NEW, ParFlat_COL_TOPOLOGY, ParFlat_COL_TOPOLOGY_NEW, Indexblk::ppp, LocusCont::strand, StringChr, StringCpy(), StringEqu(), StringEquN(), StringLen(), LocusCont::topology, and Indexblk::vernum.

Referenced by CheckOutsideEntry(), and parse_entry().

AddToIndexBlk()

static void AddToIndexBlk ( DataBlkPtr  entry, IndexblkPtr  ibp, Parser::EFormat  format  )

static

Definition at line 218 of file buf_data_loader.cpp.

References LocusCont::bases, Indexblk::bases, LocusCont::div, Indexblk::division, Parser::EMBL, format, Parser::GenBank, isalpha(), isdigit(), Indexblk::lc, len, DataBlk::len, DataBlk::mOffset, offset, StringChr, StringEquN(), and StringNCpy().

Referenced by CheckOutsideEntry(), and parse_entry().

CheckOutsideEntry()

size_t CheckOutsideEntry	(	ParserPtr	pp,
		const char *	acc,
		Int2	vernum
	)

Definition at line 436 of file buf_data_loader.cpp.

References add_entry(), AddToIndexBlk(), EntryBlk::chain, ERR_FORMAT_MissingEnd, ErrPostEx, get_sequence_text(), GetEmblBlock(), DataBlk::len, make_entry(), MemFree(), DataBlk::mOffset, DataBlk::mpData, ParFlat_ID, ParFlatEM_END, and SEV_ERROR.

Referenced by flat2asn_range_func().

get_accession_from_id()

static bool get_accession_from_id ( const CSeq_id &  id, string &  accession, int &  version  )

static

Definition at line 141 of file buf_data_loader.cpp.

References CTextseq_id_Base::GetAccession(), GetId(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetVersion(), and version.

Referenced by CBuffer_DataLoader::x_LoadData().

get_bioseq()

CRef<CBioseq> get_bioseq	(	ParserPtr	pp,
		DataBlkPtr	entry,
		const CSeq_id &	id
	)

Definition at line 272 of file buf_data_loader.cpp.

References CSeq_id::Assign(), Indexblk::bases, EntryBlk::chain, Parser::curindx, Parser::EMBL, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, Parser::entrylist, CSeq_inst_Base::eRepr_raw, eSeq_code_type_iupacna, CSeq_inst_Base::eStrand_ss, CSeq_inst_Base::eTopology_linear, Parser::farseq, Parser::format, Parser::GenBank, GetDNAConv(), GetEmblBlock(), GetEmblInstContig(), GetGenBankBlock(), GetGenBankInstContig(), GetProteinConv(), GetSeqData(), Indexblk::is_contig, DataBlk::len, DataBlk::mOffset, DataBlk::mpData, ParFlat_END, ParFlat_ID, ParFlat_LOCUS, ParFlat_ORIGIN, ParFlat_SQ, ParFlatEM_END, ParFlatSP_END, CRef< C, Locker >::Reset(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), and Parser::SPROT.

Referenced by parse_entry().

get_sequence_text()

static char* get_sequence_text ( ParserPtr  parser, const string &  accession, int  version  )

static

Definition at line 121 of file buf_data_loader.cpp.

References Parser::accver, Parser::ff_get_entry, Parser::ff_get_entry_pp, Parser::ff_get_entry_v, Parser::ff_get_entry_v_pp, and version.

Referenced by CheckOutsideEntry(), and CBuffer_DataLoader::x_LoadData().

make_entry()

static DataBlkPtr make_entry ( char *  entry_str )

static

Definition at line 353 of file buf_data_loader.cpp.

References DataBlk::len, DataBlk::mOffset, DataBlk::mpData, DataBlk::mpNext, ParFlat_ENTRYNODE, and StringLen().

Referenced by CheckOutsideEntry(), and parse_entry().

parse_entry()

static CRef<CBioseq> parse_entry ( ParserPtr  pp, char *  entry_str, const string &  accession, int  ver, const CSeq_id &  id  )

static

Definition at line 367 of file buf_data_loader.cpp.

References add_entry(), AddToIndexBlk(), Parser::curindx, Parser::entrylist, Parser::format, get_bioseq(), and make_entry().

Referenced by CBuffer_DataLoader::x_LoadData().